Intelligent Design

How Some Materialists are Blinded by Their Faith Commitments

Spread the love

Every once in a while we get one of those “aha moments” when everything comes together.  Phillip Johnson helped me to one of those moments over 20 years ago when I read this passage from an article in First Things (when that journal still permitted dissenting voices to be heard):

For scientific materialists the materialism comes first; the science comes thereafter.  We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence.  That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

Aha!  If Darwinism or something like it must be true as a matter of deduction from materialism, then evidence takes a back seat.  Dawkins once said he would prefer Darwinism even if there were no evidence to support it.  That is hard to understand until one understands Johnson’s point.

I thought about this today when a friend reminded me of this quote from Nobel laureate Jacques Monod:

“We call these [mutations] accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organisms’ hereditary structure, it necessarily follows that chance alone is at the source of every innovation of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis.”

Seriously?  No other explanation is even “conceivable”?  I can understand how someone could consider the evidence and reject ID.  I would believe they are mistaken, but not everyone is going to come to the same conclusion as I do.  I get that.  But to say that ID is not even “conceivable”?  Well, that’s just plain stupid.  Why would Monod, obviously not a stupid man, say something so dumb?  His faith commitments blinded him and stunted his imagination.  A dogmatic commitment to materialist metaphysics makes even very smart people literally blind to alternatives.  And it makes them say stupid things.

Another example:  Paraphrasing Hawking:  Because there is something, the universe can create itself from nothing.

241 Replies to “How Some Materialists are Blinded by Their Faith Commitments

  1. 1
    Aeneas Pietas says:

    Highly intelligent people have a long and storied history of saying remarkably stupid things.

  2. 2
    JDH says:

    One of the stupidest arguments given by the materialists is that they can not think of a “MECHANISM” by which the spiritual could affect the natural. The fact that they don’t realize what in reality they just pontificated is, “ASSUMING materialism, the spiritual can not affect the natural”. They do not realize that their logic rejects the spiritual as an antecedent to their initial assumption of materialism. At least to me, this is known as circular reasoning. They don’t seem to see it that way.

  3. 3
    bornagain77 says:

    The claim:

    “We call these [mutations] accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organisms’ hereditary structure, it necessarily follows that chance alone is at the source of every innovation of all creation in the biosphere.

    Vs. the evidence:

    “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns”
    James Shapiro – Evolution: A View From The 21st Century – (Page 82)

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations – Kevin Kelly – 2014
    Excerpt: What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
    On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
    http://edge.org/response-detail/25264

    Failed Darwinian Prediction – Mutations are not adaptive – Cornelius Hunter – 2015
    Excerpt: In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual.,,,
    But that assumption is now known to be false.,,,
    (References on site)
    https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
    http://www.ncbi.nlm.nih.gov/pubmed/23876611

    Duality in the human genome – November 28, 2014
    Excerpt: The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time.,,,
    According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe.
    http://medicalxpress.com/news/.....enome.html

    Molecular biology is far less random than Darwinists had presupposed:

    Darwinian Materialism vs Quantum Biology – video
    https://www.youtube.com/watch?v=LHdD2Am1g5Y

    Jim Al-Khalili, at the 2:30 minute mark of the following video states,
    “,,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate matter cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory took so long to obtain because of the technical challenges of the experiment, Katona said.
    https://phys.org/news/2015-10-quantum-coherent-like-state-biological-protein.html

  4. 4
    ET says:

    We call these [mutations] accidental; we say that they are random occurrences.

    That’s the dogma and they are sticking to it. The “right” accidents produce the appearance of design and the wrong accidents get culled.

    You know cuz we have so much evidence of accidents accumulating and creating functional machines.

    HT- bornagain77

  5. 5
    Seversky says:

    We observe mutations in the genome which are random with respect to the fitness of the organism, as far as we can tell. If they were not observed, if all organisms were perfect replicators, evolution could not and would not occur.

    We do not observe “spiritual” influences, random or otherwise, at all. In fact, since we don’t even have an operational definition of “spiritual”, it’s rather difficult to know what to look for in the first place.

    Naturalistic/materialist/physicalist accounts of the observable world have been found to work very well, in the case of quantum theory, to a very high degree of precision. All the modern technology we take for granted bears witness to that.

    If anyone knows of any “spiritualist” accounts that have proven to be as successful, feel free to put them forward.

  6. 6
    ET says:

    We observe mutations in the genome that directly affect the fitness of the organism. We also observe genetic algorithms and how well they work with their built-in guidance towards some target. So yes, we have evidence for the creative power of evolution by means of intelligent design.

  7. 7
    Barry Arrington says:

    The point of the OP is that a highly intelligent man was so blinded by his faith commitments that he implied that the design hypothesis is literally inconceivable.

    For purposes of the point I am making, it does not matter whether design is true and some materialist theory is false — or the other way around. Whichever is true, to imply that design is literally inconceivable is just plain stupid.

  8. 8
    bornagain77 says:

    as to:

    “to imply that design is literally inconceivable is just plain stupid.”

    Having “lost your mind” would also be an apt description for someone claiming that it is inconceivable that life is designed.

    “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident…you have essentially lost your mind.”
    Jay Homnick – senior editor of The American Spectator

    The World’s Ideal Storage Medium Is “Beyond Silicon” – January 20, 2017
    Excerpt: it’s easy to see why DNA is “one of the strongest candidates yet” to replace silicon as the storage medium of the future. The read-write speed is about 30 times faster than your computer’s hard drive. The expected data retention is 10 times longer. The power usage is ridiculously low, almost a billion times less than flash memory. And the data density is an astonishing 10^19 bits per cubic centimeter, a thousand times more than flash memory and a million times more than a hard disk. At that density, the entire world’s data could fit in one kilogram of DNA,,,
    “Our estimate is that we need 100,000-fold improvements to make the technology sing, and we think that’s very credible,” he says. “While past performance is no guarantee, there are new reading technologies coming onstream every year or two. Six orders of magnitude is no big deal in genomics. You just wait a bit.”…
    Scientists are seeking to match the same level of functional coherence that can be observed every second in the (DNA of our) cells of our own bodies, and of the simplest microbes. The conclusion to draw from this hardly needs to be stated.
    http://www.evolutionnews.org/2.....03443.html

    Scientists Have Stored a Movie, a Computer OS, and an Amazon Gift Card in a Single Speck of DNA
    “The highest-density data-storage device ever created.”
    – PETER DOCKRILL – 7 MAR 2017
    Excerpt: In turn, Erlich and fellow researcher Dina Zielinski from the New York Genome Centre now say their own coding strategy is 100 times more efficient than the 2012 standard, and capable of recording 215 petabytes of data on a single gram of DNA.
    For context, just 1 petabyte is equivalent to 13.3 years’ worth of high-definition video, so if you feel like glancing disdainfully at the external hard drive on your computer desk right now, we won’t judge.
    http://www.sciencealert.com/sc.....eck-of-dna

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970
    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009
    Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication.
    http://www.sciencedaily.com/re.....142957.htm

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: In the last decade, we have discovered still another aspect of the multi-dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.
    http://www.worldscientific.com.....08728_0006

    Complex grammar of the genomic language – November 9, 2015
    Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,,
    ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.
    Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.
    http://www.sciencedaily.com/re.....140252.htm

    Thus, having “lost their mind” is a thoroughly apt description of Darwinists!

    i.e. The only thing that is inconceivable is how anyone in their right mind can claim that life is not designed.

    Verse:

    Psalm 139:14
    I praise you because I am fearfully and wonderfully made;
    your works are wonderful,
    I know that full well.

  9. 9
    jdk says:

    But Johnson had his own faith commitments, for what that’s worth.

    From a speech by Johnson in Kansas City in 2001:

    We founded a movement called the Intelligent Design movement in order to explore and explain the evidence which actually does point towards the need for a designer, for a Creator, in the origin of life and its growth to complexity. …They [“the people of God” – both Protestants and Catholics] all have the need to understand whether there really is a Creator who brought about life and all its variety, or whether blind, purposeless, unassisted nature was able to do the whole job.

    This is a way of phrasing the issue that ought to bring together Protestants of different views, young-earth believers in the scriptures, old-earthers who interpret Genesis differently, even the people who take the whole thing allegorically. Again, they should have a common interest in the issue. In the beginning was the Word – in the beginning God created: true or false.

  10. 10
    Barry Arrington says:

    JDK @ 9.

    Of course Johnson had faith commitments. Everyone does. Is there a point lurking somewhere in your comment?

    While you are hunting for your point, let me clue you in on the difference between Monod and Johnson. They both had faith commitments. Johnson was self-aware enough to understand how his faith commitments affected his worldview. Monod was not. Johnson was willing to consider both sides of the origins argument. Monod was literally blind to one side.

  11. 11
    kairosfocus says:

    JDK, perhaps you need a reminder, from Lewontin:

    . . . to put a correct [–> Just who here presume to cornering the market on truth and so demand authority to impose?] view of the universe into people’s heads

    [==> as in, “we” the radically secularist elites have cornered the market on truth, warrant and knowledge, making “our” “consensus” the yardstick of truth . . . where of course “view” is patently short for WORLDVIEW . . . and linked cultural agenda . . . ]

    we must first get an incorrect view out [–> as in, if you disagree with “us” of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world [–> “explanations of the world” is yet another synonym for WORLDVIEWS; the despised “demon[ic]” “supernatural” being of course an index of animus towards ethical theism and particularly the Judaeo-Christian faith tradition], the demons that exist only in their imaginations,

    [ –> as in, to think in terms of ethical theism is to be delusional, justifying “our” elitist and establishment-controlling interventions of power to “fix” the widespread mental disease]

    and to accept a social and intellectual apparatus, Science, as the only begetter of truth

    [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

    . . . . To Sagan, as to all but a few other scientists [–> “we” are the dominant elites], it is self-evident

    [–> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

    that the practices of science provide the surest method of putting us in contact with physical reality [–> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [–> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [–> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is “quote-mined” I invite you to read the fuller annotated citation here.]

    KF

  12. 12
    EricMH says:

    @Seversky, if mutation is independent of fitness, then it’s mathematically provable mutation cannot cause increase in fitness without extremely close building blocks. This also means it should be trivial to replicate evolution with not just minor increase in functionality, but in the degree we see in biological history. However, that has never been done, e coli experiments notwithstanding.

    On the other hand, say someone was able to demonstrate macro evolution in the lab. This would merely substantiate the ID theorists point that there is an enormous amounts of active information prebuilt into the genome space, which requires intelligent intervention.

    So, there is no case for random mutation disproving ID.

  13. 13
    Bob O'H says:

    @Seversky, if mutation is independent of fitness, then it’s mathematically provable mutation cannot cause increase in fitness without extremely close building blocks.

    Can you give a citation for that? I think the statement depends on what you mean by “extremely close building blocks”, and it’s not at all clear to me what you mean by that.

  14. 14
    kairosfocus says:

    Bo’H: It’s the logic of the dynamics claimed. As, mutations are small, and to stamp into a pop need to function advantageously in an eco-niche. Very large one step changes will be overwhelmingly damaging, even fairly small ones in early embryological stages (the stuff of body plan formation) tend to be lethal. The normal “successful” mut is a break in some mechanism that confers a local advantage. Notice how antibiotic resistant bugs tend to be less viable in general and a few years ago there were reports on tomcods that were able to live with pollutants that was much the same. Sickle cell trait is a capital example, on the number one all time threat to us, malaria, the mosquito being the most dangerous animal of all. BTW, malaria drug resistance is another example. KF

  15. 15
    niwrad says:

    Materialists / atheists / evolutionists are our brothers who haven’t yet understood that there are a lot of benefits to be spiritualist / theist / ID supporter-creationist. Among them:

    (1) The infinite Principle explains all “misteries”:
    -a- cosmos and life are designed and produced by Him
    -b- our consciousness derives from the fact the we all are living forms of Himself
    -c- mathematics and sciences can be used to understand reality indeed because He is also the great Mathematician and He wants us partecipate at a certain degree to knowledge.

    (2) The infinite Principle helps us in many ways during life and in the post-mortem. Otherwise we are alone and “as leaves in the wind”. We can ask illumination on all topics and He sends us suggestions (try to believe). If in Him we trust nothing can cause fear to us and we are always happy. Seek refuge only with Him.

    (3) The infinite Principle asks us only to respect some simple rules and some moral obligations, which by the way are also those allowing social peace and order. So no war, no revolution, no evil and so on. The believers in Him have no enemies and see all people as brothers / friends. Also animals and the environment are seen as manifestation of Him, so they deserve respect. Therefore the believer is necessarily also ecological.

    Materialists / atheists / evolutionists, do not waste your time, join us in His big Tent and be happy!

  16. 16
    jdk says:

    Barry writes, “Johnson was willing to consider both sides of the origins argument.”

    Really? I don’t think I ever saw evidence of that. He wasn’t even willing, as far as I can tell, to entertain the position of theistic evolutionists, whom he called “worse than atheists because they hide their naturalism behind a veneer of religion.”

    Yes, everyone has faith commitments. That’s why it baffles me that some (including some key people here at UD) are so very certain that they are right and others with different perspectives are wrong.

  17. 17
    jdk says:

    Re 11. No kf, I don’t need the jillionth reminder of that Lewontin quote. I have absolutely nothing to do with Lewontin, and am not in agreement with him about many things.

    Sure, there are people that think as he does, but vastly more, I believe, that don’t.

  18. 18
    Barry Arrington says:

    jdk @ 16.

    The point I’ve been making is not that difficult. I wonder why you are having such a hard to time getting it. You seem to be trying to avoid it instead of attempting to understand it.

    I’ll make another run at it. Surely you agree there is a difference between (1) evaluating a claim and rejecting it; and (2) denying a claim is even conceivable.

    With respect to evolution generally and theist evolution in particular,Johnson did (1). Monod’s quote in the OP is an example of (2).

    Indeed, jdk, you are not just wrong about Johnson, you are spectacularly wrong. Johnson came to ID against his wishes. He wanted to believe Darwin; he just couldn’t get past the countervailing evidence. This is why he said: “I would love to be a Darwinist. I just can’t manage the faith commitments.”

  19. 19
    Bob O'H says:

    kf – I was hoping to see the mathematical proof, partly because the statement contradicts work like that of Basener and Sanford.

  20. 20
    jdk says:

    Barry, you are somewhat right about Johnson, although his critiques of evolution came after his strong conversion to Christianity. I know nothing about Monod, so I don’t know if he had any religious beliefs that were overcome by his exploration of what he considered the evidence that supported his eventual viewpoint.

    As a counterexample, I suspect that there are many people, including lots here at UD, that would consider it inconceivable that the Christian God doesn’t exist, and that the whole body of beliefs about Jesus and salvation are made-up myths, with not a grain of truth.

    And, there are also many people, myself included, who have examined the claims of Christianity and consider them inconceivable.

    So highlighting people with strong faith commitments to a position, claiming to have reached their position by examination of the evidence, and at some point considering it inconceivable that alternative positions are true, cuts both ways.

  21. 21
    OldAndrew says:

    Science depends on consistent observations. Nothing “spiritual” fits that.

    At the same time, given an “unexplained” phenomenon such as the existence of life and species, science does not rule out what is not observed, for the very same reason. There is no consistent observation of the non-existence of anything spiritual. (Not that it has anything to do with ID, as ID does not require anything “spiritual.”)

    Science just needs to swim in its lane. It deals in what is observed and makes no comments about what is not.

    The argument that a scientific explanation is superior to a non-scientific explanation requires, first, a scientific explanation. Despite unrelenting claims to the contrary, there are no scientific explanations of the origin of life or species. It’s a big zero. There are only assumptions.

    ID is scientific in that it is grounded in observation. What it tells us isn’t exactly an “explanation” because it doesn’t tell us how anything came to be. But that’s okay. Little pieces of knowledge are the building blocks of greater understanding.

  22. 22
    john_a_designer says:

    Recently on another thread in response to the question posed in the title of the Op: Admitted? We may never know for sure how everything began? I had this brief exchange.

    @7 I wrote: “Apparently the idea that the universe has a beginning makes some people uncomfortable. Why is that?”

    @8 JDK responded: ”Our universe had a beginning: not much of a question about that. I don’t think the Big Crunch/Big Bang again hypothesis has many followers these days.

    What I, at least, am saying (as is the OP implying) is that we really have no idea what might be the case about anything beyond/before/outside/etc. of the universe. Given that total unknowability, I don’t think we even know whether “beginningness” is a relevant concept, as the underlying concept of time may not apply either.

    [It appears to me that JDK immediately takes back with the left hand what he had just offered with his right. “Our universe had a beginning: not much of a question about that.” Which is immediately followed by well “we really have no idea what might be the case about anything.”]

    @9 Allen Keith also responded writing: “I don’t understand why that would be. Theists are fine with it. Atheists are fine with it. I think what people are uncomfortable with is that the universe would have an end. But the discomfort is at the gut level, not the intellectual level.”

    @ 12 I responded to Allen:

    Theism begins with the premise that something cannot come into existence uncaused from absolute nothing.

    Therefore, since the universe exists, it cannot have just popped into existence uncaused from nothing. Something with causal agency must have “preceded” it, though preceding it does not necessarily mean temporally preceding it. This leads us to the idea of a transcendent, self-existing or necessary being. So, if the atheist wants to believe that the universe had a beginning in an absolute sense he must believe that it either just popped into existence uncaused from absolute nothing or there is some transcendent cause whose existence cannot be proven empirically.

    If I am wrong, just provide the proof. That will be game, set, match. You win.

    https://uncommondescent.com/intelligent-design/admitted-we-may-never-know-for-sure-how-everything-began/#comment-654267

    To which JDK (not AK) responded:

    “I don’t think that the subject of this discussion is amenable to proof”: that is the point implied in the OP, and certainly my point in 1.”

    I replied:

    “Faith is belief without proof. So if you’re an atheist and you cannot prove your position, whatever you believe you believe by faith.”

    JDK responded back:

    “But I don’t have a position about what is “beyond” the known universe, other than I don’t think we can know. I am a strong agnostic as to this subject.

    I agree that theism, and any strongly held metaphysical belief system, is a held because of a faith-based choice, not because of any “proof” (or even substantial evidence) that can be given.”

    There are several points I could make about this exchange but let me concentrate on one. Both Allan Keith and JDK seem to think that in the grand scheme of things their opinions and beliefs count for something. But the truth is, if atheistic naturalism/materialism is true, their opinions and beliefs count for absolutely nothing. They are merely insignificant specks in the cosmos with no purpose, meaning or value. So why are they bothering us? Their opinions and beliefs more enlightened than anyone else’s?

    For example, what is JDK’s point of telling us, “I am a strong agnostic as to this subject”? Is he saying that because he agnostic everyone else needs to be an agnostic? But if you’re a “strong agnostic’ how can you even make a claim like that? How can someone be certain about something he strongly believes is unknowable? (Hopefully this is not another case of an infallible fallibilist.)

    Personally, I think it’s pointless to have any kind argument about the big questions unless you are seeking the Truth. Baseless opinions and beliefs are a waste of time. And while I’ll concede that we can’t come to absolute answer or “proof,” when we objectively compare two worldviews A and B one of them is a better explanation than the other. The point is that we can logically and objectively compare two competing world views and make an inference to the best explanation.

    Unfortunately our regular interlocutors for some reason always want to sabotage the approach. Why is that?

  23. 23
    jdk says:

    Recently on another thread in response to the question posed in the title of the Op: Admitted? We may never know for sure how everything began? I had this brief exchange.
    Thanks for the thoughtful response, JAD

    In your first point to me, you concluded by writing

    [It appears to me that JDK immediately takes back with the left hand what he had just offered with his right. “Our universe had a beginning: not much of a question about that.” Which is immediately followed by well “we really have no idea what might be the case about anything.”

    But you didn’t quote me completely: I wrote,

    We really have no idea what might be the case about anything beyond/before/outside/etc. of the universe.

    # That’s quite a bit different that you what you seem to have implied about my position.

    Later, I am quoted as saying,

    But I don’t have a position about what is “beyond” the known universe, other than I don’t think we can know. I am a strong agnostic as to this subject.

    I agree that theism, and any strongly held metaphysical belief system, is a held because of a faith-based choice, not because of any “proof” (or even substantial evidence) that can be given.

    Then you wrote,

    Both Allan Keith and JDK seem to think that in the grand scheme of things their opinions and beliefs count for something. But the truth is, if atheistic naturalism/materialism is true, their opinions and beliefs count for absolutely nothing.

    I don’t believe that “atheistic naturalism/materialism is true.” I can’t speak for AK.
    (I also think that the argument “if atheistic naturalism/materialism is true, their opinions and beliefs count for absolutely nothing” is a faulty argument, but that’s a different subject than what my personal beliefs are.)

    JAD writes,

    For example, what is JDK’s point of telling us, “I am a strong agnostic as to this subject”? Is he saying that because he agnostic everyone else needs to be an agnostic? [No, I’m just explaining my own position. YMMV] But if you’re a “strong agnostic’ how can you even make a claim like that? How can someone be certain about something he strongly believes is unknowable?

    I didn’t say I was certain. Saying that I have a strong belief, and being capable of backing up my belief with what I think are solid arguments, and evidence when applicable, is quite a bit different than saying I am certain that I am right. Take note of the sentence of mine you quoted above, that begins with, “I agree that theism, and any strongly held metaphysical belief system, …”

    JAD writes,

    The point is that we can logically and objectively compare two competing world views and make an inference to the best explanation.

    True, but we can differ about what we think is the best explanation, each of us “logically and objectively” comparing whatever worldviews we believe in, but coming to different conclusions.

    I am searching for knowledge and understanding, and truth with a little t, but I’m doubtful that Truth with a capital T exists. And, since I don’t think I’ve discussed this topic with you before, JAD, I will share a motto from Richard Feynman that is central to my beliefs: “I would rather live with uncertainty than believe things that are not true.” This is why I am an agnostic about metaphysical matters.

  24. 24
    Origenes says:

    jdk @

    jdk: What I, at least, am saying … is that we really have no idea what might be the case about anything beyond/before/outside/etc. of the universe. Given that total unknowability, I don’t think we even know ….

    Wait a minute. The reason as to why we suspect there being something beyond the universe is that the existence of the universe is in need for an explanation. We are looking for a cause. In that context, contrary to your claim, we do have an idea. For one thing, what we are looking for something that is capable of creating the universe.
    Secondly it must be something capable of operating outside time and space, that is, in the sense that we know them.
    A third requirement is that, given fine-tuning, it must be intelligent and being able to manipulate matter.

  25. 25
    jdk says:

    I don’t think you can know that all those assumptions are true.

    So much of your own worldview is wrapped up in them, I think, that you can’t see how other legitimate perspectives might exist.

    My point in this thread, however, is not to get involved (once again) in discussing these specifics, but to make the point that I think everyone brings some degree of faith-based metaphysical commitments to the table that can’t be proven.

  26. 26
    Barry Arrington says:

    JDK

    And, there are also many people, myself included, who have examined the claims of Christianity and consider them inconceivable.

    J, is suggest you go here:

    https://www.youtube.com/watch?v=G2y8Sx4B2Sk

  27. 27
    jdk says:

    I’m just using “inconceivable” (“not even conceivable”) because you did in the OP. It’s not a word I would use otherwise, I don’t think.

  28. 28
    Origenes says:

    jdk@

    jdk: I don’t think you can know that all those assumptions are true.

    Don’t be so pessimistic. Let’s look at the first one:

    O: …what we are looking for is something that is capable of creating the universe.

    This is backed-up by two arguments:
    1. The universe is in need of an explanation, it did not pop into being from nothingness.
    2. The cause of the universe is capable of creating the universe.
    The second is a truism. And can you come up with an objection against (1)?

    jdk: So much of your own worldview is wrapped up in them …

    Relax worrywart. We are dealing with logic 101 here.

  29. 29
    Origenes says:

    Note this:
    jdk wrote:

    … we really have no idea what might be the case about anything beyond/before/outside/etc. of the universe. Given that total unknowability, I don’t think we even know ….

    In post #24 I objected and argued that we do have an idea. And it seems to me that the idea(s) I offered make good logical sense.
    Now note what jdk tries to do:

    jdk: I don’t think you can know that all those assumptions are true.

    There is a huge chasm between “really having no idea”, “total unknowability” and having plausible ideas, but not knowing that they are true. Jdk switches between those positions. And I have offered very plausible ideas IMO. So, irrespective if I know them to be 100% true, it is not the case that we are totally in the dark, as jdk suggested — which was my point.

  30. 30

    A/mats are people of great faith in nature’s ability to do the impossible.

  31. 31
    Seversky says:

    EricMH @ 12

    @Seversky, if mutation is independent of fitness, then it’s mathematically provable mutation cannot cause increase in fitness without extremely close building blocks.

    Are you referring to the paper by Basener and Sanford that’s being discussed over at The Skeptical Zone?

    This also means it should be trivial to replicate evolution with not just minor increase in functionality, but in the degree we see in biological history. However, that has never been done, e coli experiments notwithstanding.

    I would argue that it is far from trivial to replicate in a few years of laboratory research evolutionary transformations which are estimated to have taken millions of years to happen in the wild. The best that can be done is to look for evidence of biological processes that must exist for evolution to happen at all. Observations of genetic mutations, Lenski’s LTEE, the nylon-eating bacteria and research on the peppered moth by Kettlewell and later Majerus all provide that kind of evidence.

    On the other hand, say someone was able to demonstrate macro evolution in the lab. This would merely substantiate the ID theorists point that there is an enormous amounts of active information prebuilt into the genome space, which requires intelligent intervention.

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock. In my view, it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    So, there is no case for random mutation disproving ID.

    The existence of random mutations does not disprove ID, it makes evolution possible.

  32. 32
    bornagain77 says:

    Origenes as to:

    jdk: I don’t think you can know that all those assumptions are true.

    Exactly how is it ever possible for an atheist to ever establish anything as true? Note the first word in his sentence: “I”. Everybody, including atheist, is dependent, ultimately, on the first person subjective experience of “I” in order to ever be able to differentiate whether something is true or not. Yet, in the atheist’s materialistic world view “I” simply does not exist.

    “that “You”, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased: “You’re nothing but a pack of neurons.” This hypothesis is so alien to the ideas of most people today that it can truly be called astonishing.”
    Francis Crick – “The Astonishing Hypothesis” 1994

    8.) The argument from personal existence
    1. If naturalism is true, I do not exist.
    2. I do exist!
    3. Therefore naturalism is not true.
    William Lane Craig – Is Metaphysical Naturalism Viable? – video
    http://www.youtube.com/watch?v=HzS_CQnmoLQ

    “I’m not arguing that consciousness is a reality beyond science or beyond the brain or that it floats free of the brain at death. I’m not making any spooky claims about its metaphysics. What I am saying, however, is that the self is an illusion. The sense of being an ego, an I, a thinker of thoughts in addition to the thoughts. An experiencer in addition to the experience. The sense that we all have of riding around inside our heads as a kind of a passenger in the vehicle of the body. That’s where most people start when they think about any of these questions. Most people don’t feel identical to their bodies. They feel like they have bodies. They feel like they’re inside the body. And most people feel like they’re inside their heads. Now that sense of being a subject, a locus of consciousness inside the head is an illusion. It makes no neuro-anatomical sense.”
    Sam Harris: The Self is an Illusion
    https://www.youtube.com/watch?v=fajfkO_X0l0

    Eagleton on Baggini on free will
    Excerpt: “What you’re doing is simply instantiating a self: the program run by your neurons which you feel is “you.””
    Jerry Coyne
    https://whyevolutionistrue.wordpress.com/2015/04/04/eagleton-on-baggini-on-free-will/

    Nature, as Defined Today, Cannot Be All There Is – Denyse O’Leary – October 17, 2017
    Excerpt: Thus, when we hear that evolution bred a sense of reality out of us (NPR), our perceptions of an independent reality must be illusions (Quanta), there is no “I” in “me,” (Sam Harris), our experiences of being and having a body are “‘controlled hallucinations’ of a very distinctive kind” (Aeon),,,,
    Jim Carrey summed it up best in a recent interview: “There is no me, there’s just things happening” ,,,
    https://evolutionnews.org/2017/10/nature-as-defined-today-cannot-be-all-there-is/

    “There is no self in, around, or as part of anyone’s body. There can’t be. So there really isn’t any enduring self that ever could wake up morning after morning worrying about why it should bother getting out of bed. The self is just another illusion, like the illusion that thought is about stuff or that we carry around plans and purposes that give meaning to what our body does. Every morning’s introspectively fantasized self is a new one, remarkably similar to the one that consciousness ceased fantasizing when we fell sleep sometime the night before. Whatever purpose yesterday’s self thought it contrived to set the alarm last night, today’s newly fictionalized self is not identical to yesterday’s. It’s on its own, having to deal with the whole problem of why to bother getting out of bed all over again.,,,
    – A.Rosenberg, The Atheist’s Guide to Reality, ch.10

    At the 23:33 minute mark of the following video, Richard Dawkins agrees with materialistic philosophers who say that:
    “consciousness is an illusion”
    A few minutes later Rowan Williams asks Dawkins ”If consciousness is an illusion…what isn’t?”.
    https://www.youtube.com/watch?v=HWN4cfh1Fac&t=22m57s

    “(Daniel) Dennett concludes, ‘nobody is conscious … we are all zombies’.”
    J.W. SCHOOLER & C.A. SCHREIBER – Experience, Meta-consciousness, and the Paradox of Introspection – 2004
    https://www.scribd.com/document/183053947/Experience-Meta-consciousness-and-the-Paradox-of-Introspection

    Could Consciousness be an Illusion? June 30, 2014 –
    Excerpt: “I recently participated in a conference which was unusual for a couple of reasons. Firstly it was held in a sailing boat in the Arctic. Secondly the consensus view of the conference was that consciousness is an illusion. This view, ‘illusionism’, is about as far removed from my own perspective in philosophy of mind as it is possible to get. Me the panpsychist, Martine Nida-Rümelin the substance dualist, and David Chalmers who splits his opinion between these two views, formed the official on board opposition to the hard-core reductionist majority. Somehow we managed to avoid being made to walk the plank.”,,
    Illusionism is even less plausible than solipsism: the view that my conscious mind is the only thing that exists.,,,
    http://conscienceandconsciousn.....-illusion/

    Since the fact that we really do exist as real persons is the most sure thing we can ever know about reality, (in fact as was already pointed out, since everything filters through the first person subjective experience of “I” in order to determine whether something is true or not), then the atheist, in his denial of “I”, forsakes his ability to differentiate what is true from what is false. As well as forsaking his ability to ever dictate to other people what is true.

    As Ross Douthat stated:

    The Confidence of Jerry Coyne – Ross Douthat – January 6, 2014
    Excerpt: But then halfway through this peroration, we have as an aside the confession (by Coyne) that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.) Prometheus cannot be at once unbound and unreal; the human will cannot be simultaneously triumphant and imaginary.
    http://douthat.blogs.nytimes.c.....oyne/?_r=0

    Perhaps the fact that we really exist as real persons is the most sure thing we can know about reality, and yet atheist deny this most sure thing we can know about reality, is exactly why God responded to Moses as such:

    Exodus 3:14
    And God said unto Moses, I AM THAT I AM: and he said, Thus shalt thou say unto the children of Israel, I AM hath sent me unto you.

  33. 33
    Origenes says:

    Bornagain77: … in the atheist’s materialistic world view “I” simply does not exist.

    I fully agree.
    Moreover, the materialist believes that his thoughts and actions are steered by blind particles bumping into each other. Particles that have neither the materialist nor ‘his’ thoughts nor ‘his’ actions in mind.
    Think about it, blind particles ‘decide’ what one believes, what and how one thinks and how one acts ….
    It follows, as clear as day, that there is no reason whatsoever for the materialist, or anyone else, to take the materialist, his thoughts and/or his thoughts seriously.
    In the atheist’s materialistic world view there is no place for rationality.

  34. 34
    jdk says:

    to BA77 at 32, and others. I am not an “atheist materialistic”, FWIW. I don’t think you folk’s arguments about the flaws of materialism in terms of identity, rationality, choice, etc. are valid, but that’s not my personal position.

  35. 35
    LocalMinimum says:

    Seversky @ 31:

    The LTEE only demonstrates loss of function that is locally advantageous but generally disastrous (as KF described @ 14). Larger, more fragile cell membranes allow for more surface area for nutrient absorption, loss of metabolic components for whatever they’re not being force fed lead to more efficiency, overwound DNA leading to more mutations (replication failure) to beat the rest of the population to these broken “features” first…

    The aerobic citrate metabolization is just the breaking or disabling of a switch that disables the citrate metabolization (which already existed in wild E.Coli) in the presence of oxygen. The second part, citrate transport overproduction, is likely wasteful outside of bathing in a free ocean of citrate bestowed from a higher being.

    Lenski’s bacteria are degenerate couch potatoes; “evolving” by losing their legs to better fit on the couch and one arm that would otherwise be permanently pinned to more freely reach the chip bag and controller with the other.

  36. 36
    Origenes says:

    jdk: I don’t think you folk’s arguments about the flaws of materialism in terms of identity, rationality, choice, etc. are valid.

    But you are unable to back up your opinion with reason and support, which is rather pathetic.
    For the record: I am not impressed.

  37. 37
    bornagain77 says:

    jdk at 34 you state:

    to BA77 at 32, and others. I am not an “atheist materialistic”, FWIW. I don’t think you folk’s arguments about the flaws of materialism in terms of identity, rationality, choice, etc. are valid, but that’s not my personal position.

    And herein lies the problem jdk. You tell me that you are a real person, and that your personal subjective opinions are valid for me to personally accept without question, but exactly how am I to personally know, with complete absolute 100% certainty, that you are not just a zombie going through the motions of personhood? i.e. How do I know for certain that you are really having a personal subjective experience?,, Prove it to me!

    Philosophical Zombies – cartoon
    http://existentialcomics.com/comic/11

    David Chalmers on Consciousness (Descartes, Philosophical Zombies and the Hard Problem) – video
    https://www.youtube.com/watch?v=NK1Yo6VbRoo

    You see jdk, I know for 100% fact that I really do exist, but, (especially if I personally refuse to ever accept it), there is no way for you ever to prove to me personally that you really exist as a real person and that you are not just a ‘philosophical zombie’ going through the motions of being a real person!

    Such as it is with the atheist’s refusal to ever accept any evidence for the personhood of God.

    As Alvin Plantinga pointed out years ago in “God and Other Minds”, “the evidence for God is just as good as the evidence for other minds; and conversely, if there isn’t any evidence for God, then there is also no evidence that other minds exist,,,”

    Another interesting argument comes from the leading philosopher and Christian, Alvin Plantinga—he asked, what evidence does anyone have for the existence of other people’s minds? He argued cogently that the evidence for God is just as good as the evidence for other minds; and conversely, if there isn’t any evidence for God, then there is also no evidence that other minds exist—see God and Other Minds, Cornell University Press, repr. 1990.
    http://creation.com/atheism-is-more-rational

    So jdk, since you doubt God is a real person, prove to me that you really exist as a real person and that you are not just a zombie pretending to be a person! 🙂

    I await your attempt to prove to me personally that you really exist as a real person with popcorn: 🙂 This will be fun!

    https://media1.tenor.com/images/54451401d52c0dd2fe9ee5752857d53c/tenor.gif?itemid=3579864

    Of related note: I don’t think Plantinga gets near enough credit for his body of work in Philosophy over his lifetime:

    Baylor ISR- Alvin Plantinga Interview: (2 Dozen or So Arguments) – (Nov. 7, 2014)
    https://www.youtube.com/watch?v=OxtyY2bp78E

    Table Of Contents for TWO DOZEN (OR SO) ARGUMENTS FOR GOD: THE PLANTINGA PROJECT (Summer 2017)
    I. Half a Dozen (or so) ontological (or metaphysical) arguments
    (A) The Argument from Intentionality (or Aboutness)
    • Lorraine Keller, Niagara University
    • “Propositions Supernaturalized”
    (B) The Argument from Collections
    • Chris Menzel, Texas A&M
    • “The Argument from Collections”
    (C) The Argument from (Natural) Numbers
    • Tyron Goldshmidt, Wake Forest
    • “The Argument from (Natural) Numbers”
    (D) The Argument From Counterfactuals
    • Alex Pruss, Baylor University
    • “Counterfactuals, Vagueness and God”
    (E) The Argument from Physical Constants
    • Robin Collins, Messiah College
    • “The Fine-Tuning for Discoverability”
    (F) The Naive Teleological Argument
    • C. Stephen Evans, Baylor University
    • “An Argument from Design for Ordinary People”
    (H) The Ontological Argument
    • Elizabeth Burns, Heythrop College
    • “Patching Planting’s Ontological Argument by Making the Murdoch Move”
    (I) Why is there anything at all?
    • Josh Rasmussen, Azusa Pacific; and Christopher Gregory Weaver, Rutgers University
    • “Why is There Anything?”

    II. Half a dozen Epistemological Arguments
    (J) The argument from positive epistemic status
    • Justin Barrett, Fuller Seminary
    • “Evolutionary Psychology and the Argument from Positive Epistemic Status”
    (K) The Argument from the confluence of proper function and reliability
    • Alex Arnold, The John Templeton Foundation
    • “Is God the Designer of our Cognitive Faculties? Evaluating Plantinga’s Argument”
    (L) The Argument from Simplicity and (M) The Argument from Induction
    • Bradly Monton, Independent Scholar
    • “Atheistic Induction by Boltzmann Brains”

    (N) The Putnamian Argument (the Argument from the Rejection of Global Skepticism)[also, (O) The Argument from Reference and (K) The Argument from the Confluence of Proper Function and Reliability]
    • Even Fales, University of Iowa
    • “Putnam’s Semantic Skepticism and the Epistemic Melt-Down of Naturalism: How Defeat of Putnam’s Puzzle Provides a Defeater for Plantinga’s Self-Defeat Argument Against Naturalism”

    (N) The Putnamian Argument, (O) The Argument from Reference, and (P) The Kripke-Wittgenstein Argument from Plus and Quus
    • Dan Bonevac, University of Texas
    • “Arguments from Knowledge, Reference, and Content”

    (Q) The General Argument from Intuition.
    • Rob Koons, University of Texas at Austin
    • “The General Argument from Intuition”
    III. Moral arguments
    (R) Moral Arguments (actually R1 to Rn)
    • David Baggett, Liberty University
    • “An Abductive Moral Argument for God”

    (R*) The argument from evil.
    • Hud Hudson, Western Washington University
    • “Felix Culpa!”

    IV. Other Arguments
    (S) The Argument from Colors and Flavors
    • Richard Swinburne, Oxford University
    • “The Argument from Consciousness”
    (T) The Argument from Love and (Y) The Argument from the Meaning of Life
    • Jerry Walls, Houston Baptist University
    • “The God of Love and the Meaning of Life”
    (U) The Mozart Argument and (V) The Argument from Play and Enjoyment
    • Philip Tallon, Houston Baptist University
    • “The Theistic Argument from Beauty and Play”
    (W) Arguments from providence and from miracles
    • Tim McGrew, Western Michigan University
    • “Of Miracles: The State of the Art and the Uses of History”
    (X) C.S. Lewis’s Argument from Nostalgia
    • Todd Buras, Baylor University and Mike Cantrell
    • “A New Argument from Desire”
    (Z) The Argument from (A) to (Y)
    • Ted Poston, University of South Alabama
    • “The Argument from So Many Arguments”
    V. “Or so”: Three More Arguments
    The Kalam Cosmological Argument
    • William Lane Craig, Houston Baptist University
    • “The Kalam Cosmological Argument”
    The Argument from Possibility
    • Brian Leftow, Oxford University
    • “The Argument from Possibility”
    The Argument from the Incompleteness of Nature
    • Bruce Gordon, Houston Baptist University
    • “The Necessity of Sufficiency: The Argument from the Incompleteness of Nature”
    https://global.oup.com/academic/product/two-dozen-or-so-arguments-for-god-9780190842215?cc=us&lang=en&

  38. 38
    groovamos says:

    Seversky: We observe mutations in the genome which are random with respect to the fitness of the organism, as far as we can tell.

    Seversky: Need I provide a list of all the medical, scientific and technological advances that we all take for granted but which are founded on a naturalistic model of the world? –> https://uncommondescent.com/philosophy/philosopher-on-what-is-wrong-with-naturalism/

    groovamos: Naturalistic science has not demonstrated absolute statistical independence among so-called random mutations which give rise to novel form or function, and likely will never devise a way to do so. The best that science can do here is to presume the ‘null hypothesis’ that such are presumed random until proven otherwise. This relegates Darwinian theory to having hypothetical basis instead of being a profound “advance”. (same link)

    Seversky: (crickets)

    groovamos: BTW Seversky I notice that you didn’t want to touch my example of so-called random mutations which have never been proved to have stochastic basis.

    Seversky: (crickets)

  39. 39

    Seversky @31 said:

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock. In my view, it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    I don’t accept that the notion of “random mutation” or “naturalism” as commonly understood, is a property of the genome or an organism or a piece of rock. In my view it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    You’re being hypocritical here, saying that your preferred map (naturalism-based) is the territory, while another (design-based) only represents it.

    The existence of random mutations does not disprove ID, it makes evolution possible.

    Or, designed systems and controls which account for and use, among other things, random mutations, makes evolution possible.

    JDK @35 said:

    My point in this thread, however, is not to get involved (once again) in discussing these specifics, but to make the point that I think everyone brings some degree of faith-based metaphysical commitments to the table that can’t be proven.

    All arguments and systems of evidence begin, ultimately, with faith-based commitments. The question is, where do those axiomatic assumptions lead? Do they lead to good conclusions and good descriptions? Or do they force you to believe and say self-contradictory and unsupportable things and deny the obvious? Do your faith-based assumptions force you to deny your free will, abandon the concept of truth, utter hypocritical statements,and willfully blind yourself to evidence and potential explanations?

    Do they make you say things like “Even if we found a fully working, mechanized timepiece in existence dating back to the beginning of the universe with no other evidence whatsoever around, we’d have NO EVIDENCE of intelligent design at the beginning of the universe?”

    To say that “there no evidence of a designer” around at the time of the origin of a highly complex, functional, code-driven mechanism is beyond absurd. You would not say that if we were talking about anything other than biological organisms, I don’t think. Would you?

  40. 40

    If the materialists were to find any other kind of highly complex, functional, code-driven mechanism, they would not hesitate to infer that the most likely explanation was some form of intelligent being created it.

    Materialists consider biological organisms to be pretty much “the same as” any other kind of matter in the world – just collections of various forms of matter.

    This raises the question: why are materialists so insistent that the highly complex, functional, code-driven mechanisms we find in biological organisms **are not** best explained by an intelligent being creating them?

    What’s so special about biological organisms? To a materialist, they’re just machines. Highly complex, functional machines. In every other case, they would think an intelligent designer would be the best explanation and wouldn’t even consider the idea that such a machine simply put itself together from scratch.

    Can you imagine a materialist claiming that a 747 or a battleship put itself together from scratch without the aid of an intelligent designer? It would be enormously ludicrous, foolish beyond belief.

    Why the complete turnabout when it comes to biological machines, which are far, far more complex and highly functional than any machine humans ever built? What bizarre faith commitment has them treating biological machines so different from any other kind of machine, when to them there is no real difference in principle?

  41. 41
    bornagain77 says:

    groovamos, I hope you don’t mind if I touch upon this outlandish claim from Seversky:

    Seversky: Need I provide a list of all the medical, scientific and technological advances that we all take for granted but which are founded on a naturalistic model of the world?

    Yet the fact of the matter is that there is not one medical, scientific or technological advance that Seversky can point to that supports his presupposed ‘naturalistic model of the world’. In fact all medical, scientific and technological advances point to Intelligent Design. Moreover, all medical, scientific and technological advances provide fairly compelling evidence that we are indeed made in the ‘image of God’.

    Although the purported evidence for human evolution is far weaker and illusory than most people realize,,,

    “Contested Bones” (Part 1 – Prologue and Chapter 1 “Power of the Paradigm”) 1-27-2018 by Paul Giem
    https://www.youtube.com/watch?v=e6ZOKj-YaHA&list=PLHDSWJBW3DNU_twNBjopIqyFOwo_bTkXm

    The Human-Ape Missing Link — Still Missing – July 18, 2017
    Excerpt: Here is a long, substantive, and interesting article from the BBC — “We still have not found the missing link between us and apes.” It is interesting for two reasons.
    – 1. It admits that we haven’t found anything that resembles the last common ancestor (LCA) between humans and apes, what author Colin Barras calls the “missing link.”
    – 2. It admits that it’s hard to even agree on what the LCA might have looked like. —
    What it doesn’t do is admit the even bigger problem: that we don’t even have transitional forms between Australopithecus and Homo. This is a major omission.,,,,
    https://evolutionnews.org/2017/07/the-human-ape-missing-link-still-missing/

    (March 2018)
    1. The DNA similarity (between chimps and humans) is not nearly as close to 99% as Darwinists have falsely portrayed it to be.
    2. Even if DNA were as similar as Darwinists have falsely portrayed it to be, the basic ‘form’ that any organism may take is not reducible to DNA, (nor is the basic ‘form’ reducible to any other material particulars in molecular biology, (proteins, RNAs, etc.. etc.. ,,), that Darwinists may wish to invoke. That is to say, ‘you can mutate DNA til the cows come home’ and you will still not achieve a fundamental change in the basic form of an organism. And since the basic ‘form’ of an organism is forever beyond the explanatory power of Darwinian mechanisms, then any belief that Darwinism explains the ‘transformation of forms’ for all of life on earth is purely a pipe dream that has no experimental basis in reality.
    3. To further drive this point home, Dolphins and Kangaroos, although being very different morphologically from humans, are found to have very similar DNA sequences.
    4. Where differences are greatest between chimps and humans are in alternative splicing patterns. In fact ., due to alternative slicing, “Alternatively spliced isoforms,,, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,,” and “As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms,,”
    5. Although the behavioral differences between man and apes are far greater than many Darwinists are willing to concede, the one difference that most dramatically separates man from apes, i.e. our ability to speak, is the one unique attribute that leading Darwinists themselves admit that they have no clue how it could have possibly evolved, and is also the one attribute that most distinctly indicates that we are indeed ‘made in the image of God’.
    https://uncommondescent.com/intelligent-design/comparing-human-and-chimp-dna-using-a-software-analogy/#comment-654633

    Although the purported evidence for human evolution is far weaker and illusory than most people realize, it is interesting to note that leading Darwinists themselves admit that they have no clue how evolution could have produced the particular trait of language in humans.

    Leading Evolutionary Scientists Admit We Have No Evolutionary Explanation of Human Language – December 19, 2014
    Excerpt: Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved.,,,
    (Marc Hauser, Charles Yang, Robert Berwick, Ian Tattersall, Michael J. Ryan, Jeffrey Watumull, Noam Chomsky and Richard C. Lewontin, “The mystery of language evolution,” Frontiers in Psychology, Vol 5:401 (May 7, 2014).)
    Casey Luskin added: “It’s difficult to imagine much stronger words from a more prestigious collection of experts.”
    http://www.evolutionnews.org/2.....92141.html

    Tom Wolfe was so taken aback by this confession by leading Darwinists that he wrote a book entitled ‘Kingdom of Speech’ on the subject. The following quote provides an overview of Tom Wolfe’s main argument in his book:

    “Speech is not one of man’s several unique attributes—speech is the attribute of all attributes! Speech is 95 percent plus of what lifts man above animal! Physically, man is a sad case. His teeth, including his incisors, which he calls eyeteeth, are baby-size and can barely penetrate the skin of a too-green apple. His claws can’t do anything but scratch him where he itches. His stringy-ligament body makes him a weakling compared to all the animals his size. Animals his size? In hand-to-paw, hand-to-claw, or hand-to-incisor combat, any animal his size would have him for lunch. Yet man owns or controls them all, every animal that exists, thanks to his superpower: speech.”
    —Tom Wolfe, in the introduction to his book, The Kingdom of Speech

    In other words, although humans are fairly defenseless creatures in the wild compared to other creatures, such as lions, bears, and sharks, etc.., nonetheless, humans have, completely contrary to Darwinian ‘survival of the fittest’ thinking, managed to become masters of the planet, not by brute force, but simply by our unique ability to communicate information and, more specifically, infuse information into material substrates,,
    Here are a couple of articles which clearly get this ‘top-down’ infusion of immaterial information into material substrates point across:

    Describing Nature With Math By Peter Tyson – Nov. 2011
    Excerpt: Mathematics underlies virtually all of our technology today. James Maxwell’s four equations summarizing electromagnetism led directly to radio and all other forms of telecommunication. E = mc2 led directly to nuclear power and nuclear weapons. The equations of quantum mechanics made possible everything from transistors and semiconductors to electron microscopy and magnetic resonance imaging.
    Indeed, many of the technologies you and I enjoy every day simply would not work without mathematics. When you do a Google search, you’re relying on 19th-century algebra, on which the search engine’s algorithms are based. When you watch a movie, you may well be seeing mountains and other natural features that, while appearing as real as rock, arise entirely from mathematical models. When you play your iPod, you’re hearing a mathematical recreation of music that is stored digitally; your cell phone does the same in real time.
    “When you listen to a mobile phone, you’re not actually hearing the voice of the person speaking,” Devlin told me. “You’re hearing a mathematical recreation of that voice. That voice is reduced to mathematics.”
    http://www.pbs.org/wgbh/nova/p.....-math.html

    Recognising Top-Down Causation – George Ellis
    Excerpt: page 5: A: Causal Efficacy of Non Physical entities:
    Both the program and the data are non-physical entities, indeed so is all software. A program is not a physical thing you can point to, but by Definition 2 it certainly exists. You can point to a CD or flashdrive where it is stored, but that is not the thing in itself: it is a medium in which it is stored.
    The program itself is an abstract entity, shaped by abstract logic. Is the software “nothing but” its realisation through a specific set of stored electronic states in the computer memory banks? No it is not because it is the precise pattern in those states that matters: a higher level relation that is not apparent at the scale of the electrons themselves. It’s a relational thing (and if you get the relations between the symbols wrong, so you have a syntax error, it will all come to a grinding halt). This abstract nature of software is realised in the concept of virtual machines, which occur at every level in the computer hierarchy except the bottom one [17]. But this tower of virtual machines causes physical effects in the real world, for example when a computer controls a robot in an assembly line to create physical artefacts.
    Excerpt page 7: The assumption that causation is bottom up only is wrong in biology, in computers, and even in many cases in physics, ,,,
    The mind is not a physical entity, but it certainly is causally effective: proof is the existence of the computer on which you are reading this text. It could not exist if it had not been designed and manufactured according to someone’s plans, thereby proving the causal efficacy of thoughts, which like computer programs and data are not physical entities.
    http://fqxi.org/data/essay-con.....s_2012.pdf

    What is more interesting still, besides the fact that humans have a unique ability to understand and create information and have become ‘masters of the planet’ through the ‘top-down’ infusion of information into material substrates, is the fact that, due to advances in science, both the universe and life itself are now found to be ‘information theoretic’ in their foundational basis.

    Renowned physicist John Wheeler stated “in short all matter and all things physical are information-theoretic in origin and this is a participatory universe”.

    “it from bit” Every “it”— every particle, every field of force, even the space-time continuum itself derives its function, its meaning, its very existence entirely—even if in some contexts indirectly—from the apparatus-elicited answers to yes-or-no questions, binary choices, bits. “It from bit” symbolizes the idea that every item of the physical world has a bottom—a very deep bottom, in most instances, an immaterial source and explanation, that which we call reality arises in the last analysis from the posing of yes-no questions and the registering of equipment—evoked responses, in short all matter and all things physical are information-theoretic in origin and this is a participatory universe.”
    – Princeton University physicist John Wheeler (1911–2008) (Wheeler, John A. (1990), “Information, physics, quantum: The search for links”, in W. Zurek, Complexity, Entropy, and the Physics of Information (Redwood City, California: Addison-Wesley))

    In the following article, Anton Zeilinger, a leading expert in quantum mechanics, stated that ‘it may very well be said that information is the irreducible kernel from which everything else flows.’

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.”
    Anton Zeilinger – a leading expert in quantum mechanics:

    In the following video at the 48:24 mark, Anton Zeilinger states that “It is operationally impossible to separate Reality and Information” and he goes on to note, at the 49:45 mark, the Theological significance of “In the Beginning was the Word” John 1:1

    48:24 mark: “It is operationally impossible to separate Reality and Information”
    49:45 mark: “In the Beginning was the Word” John 1:1
    Prof Anton Zeilinger speaks on quantum physics. at UCT – video
    http://www.youtube.com/watch?v=s3ZPWW5NOrw

    Vlatko Vedral, who is a Professor of Physics at the University of Oxford, and who is also a recognized leader in the field of quantum mechanics, states, The most fundamental definition of reality is not matter or energy, but information–

    “The most fundamental definition of reality is not matter or energy, but information–and it is the processing of information that lies at the root of all physical, biological, economic, and social phenomena.”
    Vlatko Vedral – Professor of Physics at the University of Oxford, and CQT (Centre for Quantum Technologies) at the National University of Singapore, and a Fellow of Wolfson College – a recognized leader in the field of quantum mechanics.

  42. 42
    bornagain77 says:

    Moreover, besides being foundational to physical reality, information, as Intelligent Design advocates have been pointing out to Darwinists for years, is also foundational to biological life. Here are a few references to get that point across:

    Information Enigma (Where did the information in life come from?) – – Stephen Meyer – Doug Axe – video
    https://www.youtube.com/watch?v=aA-FcnLsF1g

    Complex grammar of the genomic language – November 9, 2015
    Excerpt: The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings explain why the human genome is so difficult to decipher –,,,
    ,,, in their recent study in Nature, the Taipale team examines the binding preferences of pairs of transcription factors, and systematically maps the compound DNA words they bind to.
    Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.
    http://www.sciencedaily.com/re.....140252.htm

    Information is Physical (but not how Rolf Landauer meant) – video
    https://www.youtube.com/watch?v=H35I83y5Uro

    It is hard to imagine a more convincing scientific proof that we are made ‘in the image of God’ than finding both the universe, and life itself, are both ‘information theoretic’ in their foundational basis, and that we, of all the creatures on earth, uniquely possess an ability to understand and create information, and, moreover, have come to ‘master the planet’ precisely because of our unique ability infuse information into material substrates.

    Humanity – Chemical Scum or Made in the Image of God? – video
    https://youtu.be/ElBWAwjPzyM

    Genesis 1:26
    And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth.

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by Him, and without Him was not anything made that was made. In Him was life, and that life was the Light of men.

    Perhaps a more convincing evidence that we are made in the image of God and that our lives have meaning and purpose could be if God Himself became a man, defeated death on a cross, and then rose from the dead to prove that He was indeed God.

    But who has ever heard of such a thing as that?

    “Christianity is not merely religious truth, it is total truth — truth about the whole of reality.”
    – Francis Schaeffer –

    Copernican Principle, Agent Causality, and Jesus Christ as the “Theory of Everything”
    https://www.youtube.com/watch?v=NziDraiPiOw

    Turin Shroud Hologram Reveals The Words “The Lamb”
    https://www.youtube.com/watch?v=4Tmka1l8GAQ

    Colossians 1:15-20
    The Son is the image of the invisible God, the firstborn over all creation. For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together. And he is the head of the body, the church; he is the beginning and the firstborn from among the dead, so that in everything he might have the supremacy. For God was pleased to have all his fullness dwell in him, and through him to reconcile to himself all things, whether things on earth or things in heaven, by making peace through his blood, shed on the cross.

    Matthew 28:18
    Jesus came to them and said: I have been given all authority in heaven and on earth!

  43. 43

    WJM @ 40: “If the materialists were to find any other kind of highly complex, functional, code-driven mechanism, they would not hesitate to infer that the most likely explanation was some form of intelligent being created it.”

    True indeed. Obvious hypocrisy.

  44. 44
    EricMH says:

    @Bob O’H & Seversky, what I mean by close building blocks is that a very small number of bits need to flip to continue hitting new units of functionality. Otherwise, organisms will fail to evolve and rapidly die off.

    If you want a quantitative demonstration, I wrote a very simple Python simulation of the destructiveness of random mutation.

    https://repl.it/@EricHolloway/Evolution-Doesnt-Work

    Yes, evolution supposedly took millions of years, but if random mutation is all it takes, then we can replicate evolution easily in silico, and simulation millions, billions or trillions of years in minutes or hours. I completed my MSc under one of the world experts in evolutionary algorithms, and evolutionary algorithms are definitely not that effective. One example he liked his students to do is compare evolutionary algorithms to random search, and notice there wasn’t a big difference in performance.

    If evolution does work, then the only reason it works is not because of random mutation, but because the fitness landscape has an extremely good neighborhood function. In which case, random mutation is besides the point. Pretty much any method of searching the neighborhood would work, as long as it is not purposefully designed to avoid good neighbors.

    If the fitness landscape is indeed so finely constructed, then this is exactly what ID predicts, and would confirm ID.

  45. 45

    Seversky said:

    Need I provide a list of all the medical, scientific and technological advances that we all take for granted but which are founded on a naturalistic model of the world?

    Providing a list that you or others claim to be “founded on a naturalistic model of the world” is not the same as showing how any of those advances are actually founded on that model.

    Given that no “naturalistic model” can as yet provide for the existence of consciousness, free will and the capacity for truth discernment necessary to even begin to make such an argument and for it to have any value, I suggest you begin there.

    Then, you can continue by explaining the existence of the force constants and natural laws that undergird every “natural” effect and relationship that provides for such advances.

  46. 46
    Bob O'H says:

    @Bob O’H & Seversky, what I mean by close building blocks is that a very small number of bits need to flip to continue hitting new units of functionality. Otherwise, organisms will fail to evolve and rapidly die off.

    If you want a quantitative demonstration, I wrote a very simple Python simulation of the destructiveness of random mutation.

    https://repl.it/@EricHolloway/Evolution-Doesnt-Work

    Hm, that’s not a proof. It also ignores beneficial mutations, so it doesn’t show anything about finding new islands of functionality.

  47. 47
    ET says:

    Beneficial is relative, Bob. Even a loss of function is beneficial. Loss of eyes and limbs are beneficial. What you don’t have is a mechanism capable of producing eyes and limbs in the first place.

  48. 48
    bornagain77 says:

    as to:

    “It also ignores beneficial mutations,”

    Now if there was anything that ever was a ‘faith commitment’ on the part of atheists, it is the atheist’s completely unfounded, yet steadfast, belief that rare beneficial mutations will somehow save the day against the onslaught of the overwhelming rate of detrimental mutations:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    http://www.worldscientific.com.....08728_0006

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    Gloves Off — Responding to David Levin on the Nonrandom Evolutionary Hypothesis – Lee M. Spetner – Sept. 2016
    Excerpt: I wrote in this book (as well in an earlier book) that there is no example of a random mutation that adds heritable information to the genome, and that statement still stands. The statement is important because evolution is about building up information (Spetner 1964, 1968, 1970). Some have offered what they think are counterexamples of my statement, but they are often not of random mutations at all, or they otherwise fail to be valid counterexamples.
    Levin finds the statement astonishing, and it may well astonish someone who believes evolutionary theory represents reality. But it happens to be true, and I am not surprised that it astonishes him because it deals a deathblow to evolutionary theory.
    http://www.evolutionnews.org/2.....03168.html

    The Human Gene Mutation Database
    The Human Gene Mutation Database (HGMD®) represents an attempt to collate known (published) gene lesions responsible for human inherited disease.
    Mutation total (as of Feb. 17 , 2018) – 220270
    http://www.hgmd.cf.ac.uk/ac/

    Critic ignores reality of Genetic Entropy – Dr John Sanford – 7 March 2013
    Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.].
    African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare!
    http://creation.com/genetic-entropy

    Genetic Entropy – references to several peer reviewed numerical simulations analyzing and falsifying all flavors of Darwinian evolution (neutral theory included),, (via John Sanford and company)
    http://www.geneticentropy.org/#!properties/ctzx

    Geneticist Corrects Fisher’s Theorem, but the Correction Turns Natural Selection Upside Down – December 22, 2017 | David F. Coppedge
    A new paper corrects errors in Fisher’s Theorem, a mathematical “proof” of Darwinism. Rather than supporting evolution, the corrected theorem inverts it.
    Excerpt: The authors of the new paper describe the fundamental problems with Fisher’s theorem. They then use Fisher’s first principles, and reformulate and correct the theorem. They have named the corrected theorem The Fundamental Theorem of Natural Selection with Mutations. The correction of the theorem is not a trivial change – it literally flips the theorem on its head. The resulting conclusions are clearly in direct opposition to what Fisher had originally intended to prove.,,,
    The authors of the new paper realized that one of Fisher’s pivotal assumptions was clearly false, and in fact was falsified many decades ago. In his informal corollary, Fisher essentially assumed that new mutations arose with a nearly normal distribution – with an equal proportion of good and bad mutations (so mutations would have a net fitness effect of zero). We now know that the vast majority of mutations in the functional genome are harmful, and that beneficial mutations are vanishingly rare. The simple fact that Fisher’s premise was wrong, falsifies Fisher’s corollary. Without Fisher’s corollary – Fisher’s Theorem proves only that selection improves a population’s fitness until selection exhausts the initial genetic variation, at which point selective progress ceases. Apart from his corollary, Fisher’s Theorem only shows that within an initial population with variant genetic alleles, there is limited selective progress followed by terminal stasis.,,,
    The authors observe that the more realistic the parameters, the more likely fitness decline becomes.
    https://crev.info/2017/12/geneticist-corrects-fishers-theorem/

  49. 49

    ET @ 47: Good points. A/mats never seem to get that very simple logic.

  50. 50
    ET says:

    Truth Will Set You Free-

    Unguided evolution has a chance if and only if the Creation view of origins is correct. Meaning humans have actually devolved since that origins

  51. 51
    Mung says:

    Seversky:

    We observe mutations in the genome which are random with respect to the fitness of the organism, as far as we can tell.

    ok, but that’s not what Monod wrote. His statement was unqualified. Where does he mention anything to do with being “relative to the fitness of the organism”?

    He is making a much stronger claim.

  52. 52
    jdk says:

    Seversky wrote above,

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock. In my view, it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    This is an interesting point. I think it distinguishes those that believe that the world is what it is and our knowledge about it is an abstract overlay on top of it from those that believe that concepts have an independent, and at times primary precedence over physical reality. (That’s a messy sentence, but I have no time for thinking very much about any of this today.)

    The Platonic / non-Platonic dichotomy is, I think, the fundamental philosophical divide between the various viewpoints that get expressed here at UD.

  53. 53
    ET says:

    Seversky:

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock.

    Methinks that you don’t understand the word “information”. It is in the standard and accepted definitions of “information” that we find:

    b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (such as nucleotides in DNA or binary digits in a computer program) that produce specific effects

    And Dr Crick provided:

    “Information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein.”

    So there really isn’t any question that information is a property of living organisms.

  54. 54
    ET says:

    It’s not a code.

    It’s not information.

    It is not IC.

    OK maybe it is IC but nature did it.

    What other anti-ID evidence-free declarations are there?

  55. 55
    Allan Keith says:

    ET,

    So there really isn’t any question that information is a property of living organisms.

    By that definition, there is little doubt that information is found in living organisms. But, using the same definition, it is also found in inanimate matter.

  56. 56
    ET says:

    Yes, Allan. Information is everywhere. This universe wouldn’t exist without it.

  57. 57
    Allan Keith says:

    ET,

    Yes, Allan. Information is everywhere. This universe wouldn’t exist without it.

    Then why is it being used as an indication of design? Am I missing something?

  58. 58
    ET says:

    Allan Keith:

    Then why is it being used as an indication of design? Am I missing something?

    Everything, apparently. Information only comes from intelligence, ie a mind. The specific arrangements of information that is required to produce living organisms only comes from intelligence. The specific arrangements of information to produce the laws of physics and chemistry only comes from intelligence.


    “Information is information, neither matter nor energy. Any materialism which disregards this, will not survive one day.”
    Norbert Weiner

  59. 59
    LocalMinimum says:

    Information denial is not really an option for an A/Mat who isn’t operating on blind faith. For the universe to remain “natural” (as materialists define it), it must consist of that which can be modeled; to allow it to escape our comprehension, to grant that there are mechanics operating in dark reaches beyond the illumination of the lantern of science (beyond the eyes and cognition of “clever apes”), is to make the known “natural” a subset of reality; and to allow its complement with respect to reality, the dreaded “supernatural”, to move in next door. An eternal gap, of unknown dimension, for God to reside.

    Thus, everything must ultimately be definable as a parameterization within some model; which would be information. So a rational, factually rooted materialism would have to demand everything ultimately be reducible to information.

    Not to say that it would be sufficient; just necessary.

  60. 60
    ET says:

    LocalMinimum- They don’t deny it they just say “it’s an abstract construct that we invented”

  61. 61
    jdk says:

    Yes, that was Seversky’s point in 31, but putting “just” in the sentence minimizes the point. All of our knowledge is composed of abstract concepts that we have created/invented. The real world, in all it’s finely detailed existence, is vastly bigger, more complicated, and more nuanced than our attempts to compress it into understandable human knowledge.

  62. 62
    EricMH says:

    @Bob O’H the simulation just shows how mutation is destructive to complexity. The building blocks is a different topic, but also easy to simulate. Perhaps when I have more time I’ll write you a sim.

    Anyways, the point is that evolution is easy to simulate on a computer, at much greater timescales than in the history of our world. Even then, it just doesn’t do that much. If species did evolve, it is not thanks to evolution, but thanks to incredible amounts of built in pathways in the search landscape.

  63. 63
    jdk says:

    Eric writes,

    the point is that evolution is easy to simulate on a computer

    I think this statement is a good example of my point in 61, because it is so wrong. The complexity of millions of organisms, continually interacting with a complex environment, over thousands of generations, with genomes transforming into phenomes, is not easy to simulate. Simulations on a computer are vast, vast simplifications of reality, emphasizing a few points that we think we understand and not accounting for many that we do not.

  64. 64
    EricMH says:

    @JDK, you are no longer talking about evolution, you are talking about the biosphere. ID agrees there is a huge amount of information in the biosphere, none of it comes from evolution.

    Evolution itself, the part that matters for this debate, is random mutation + natural selection. That is trivial to simulate on a computer.

  65. 65
    EricMH says:

    @Bob O’H, here is a simple way to simulate the building blocks.

    As usual we represent DNA with a bitstring: 101010101010.

    A building block looks like this: 10*0***10

    The *s designate ‘don’t care’ bits in the building block. A building block of length L with N *s covers 2^(N-L) of the search space.

    From this we can calculate how likely an organism will randomly mutate into another building block under a variety of scenarios.

  66. 66
    jdk says:

    Eric, your simulation says nothing about how the mutations will affect the overall organism, or how this goes on over huge numbers of organisms and generations (with therefore there being different genomes in succeeding generations) or the huge complexity of an actual genome and the way genes interact with each other, and so on.

    I’m by no means very knowledgable about all theses details: i just know your model is a huge simplification that can not truly be said to simulate evolution.

  67. 67
    EricMH says:

    @JDK, if the landscape changes, we can simulate that by changing the set of building blocks.

    Of course, we are not directly simulating our biological world. But it will tell us mathematically what our biological world must look like if our hypothesized form of evolution is going to work. And what it looks like is an extraordinarily integrated set of building blocks, the likes of which could not themselves be assembled randomly, i.e. Dembski’s Vertical No Free Lunch Theorem.

    Merely saying, “but it is not real living organisms” is a cop out.

  68. 68
    Origenes says:

    EricMH @

    EricMH: If species did evolve, it is not thanks to evolution, but thanks to incredible amounts of built in pathways in the search landscape.

    In sync with Dembski when he writes about Dawkins’ ‘methinks it is like a weasel’:

    Dawkins asks his readers to suppose an evolutionary algorithm that evolves the target phrase. But such an evolutionary algorithm privileges the target phrase by adapting the fitness landscape so that it assigns greater fitness to phrases that have more corresponding letters in common with the target.
    And where did that fitness landscape come from? Such a landscape potentially exists for any phrase whatsoever, and not just for METHINKS IT IS LIKE A WEASEL. Dawkins’s evolutionary algorithm could therefore have evolved in any direction, and the only reason it evolved to METHINKS IT IS LIKE A WEASEL is that he carefully selected the fitness landscape to give the desired result. Dawkins therefore got rid of Shakespeare as the author of METHINKS IT IS LIKE A WEASEL, only to reintroduce him as the (co)author of the fitness landscape that facilitates the evolution of METHINKS IT IS LIKE A WEASEL.

    Later in the article Dembski quotes Kauffman:

    As Kauffman writes in Investigations:

    If mutation, recombination, and selection only work well on certain kinds of fitness landscapes, yet most organisms are sexual, and hence use recombination, and all organisms use mutation as a search mechanism, where did these well-wrought fitness landscapes come from, such that evolution manages to produce the fancy stuff around us?

    According to Kauffman, “No one knows.”

  69. 69
    jdk says:

    Eric, it sounds to me that you are building your preconceived conclusion into your simplistic model, but i’m ready to let further discussion go.

  70. 70
    bornagain77 says:

    Well, well, well,, looky see what Pross himself had to say about Turner’s new book:

    What Evolution “Controversy”? Scott Turner Gets High Praise from Quarterly Review of Biology – March 26, 2018
    Excerpt: Here, for example, is a review in the current volume of The Quarterly Review of Biology praising Scott Turner’s book, Purpose and Desire: What Makes Something “Alive” and Why Modern Darwinism Has Failed to Explain It.
    The,, review is striking.
    “For those who still believe that the fundamentals of modern biology were firmly established by Darwin’s monumental theory of evolution a century and a half ago, and fine-tuned by neo-Darwinism some seven decades later, J. Scott Turner’s provocatively titled book Purpose & Desire is a further reminder that [biology’s] very nature remains mired in controversy and uncertainty.”,,,
    “The author…proceeds to build on this theme to argue three main points, all controversial in varying degrees. First, that the central thesis of neo-Darwinism, namely, that evolution is the result of what Turner labels a “soulless lottery” (p. 292) of the gene pool, rests on the shakiest of grounds and is long due for revision.”,,,
    “What makes the book so worthwhile and thought-provoking is, however, that Turner is a deeply knowledgeable biologist, well versed in the intimate details of evolutionary theory and the convoluted path the evolutionary debate has taken over the past 150 years.”
    https://evolutionnews.org/2018/03/what-evolution-controversy-scott-turner-gets-high-praise-from-quarterly-review-of-biology/

    (The Darwinian Gestapo better quickly send their henchmen to put this ‘loose cannon’ Turner guy in his place.)

  71. 71
    EricMH says:

    @JDK, I understand these discussions are very tiring and circular, and I respect your desire to step out. For anyone else, I’d be interested to know how the model fails to capture evolution. Simple does not mean simplistic. E.g. f=ma is simple, but extremely deep.

    Phenotype comes from genotype. Genotype is composed of 4 bases, and we can represent that in binary. Different bits in the genome have different effects on fitness relative to the surrounding population and environment, and we can represent fitness as a probability the organism will survive.

    While the above is simple, I do not see what is missing, it is not simplistic. There is plenty of complex interaction that happens outside this formulation: environment, niches, worldwide catastrophes, etc. But that can all be represented as a function of the history of DNA ‘bitstrings’. And, while we cannot easily represent the specific values the function will take at different time stamps (the complexity you speak of), we can still see what sort of mathematical characteristics must obtain for evolution to reproduce what we see, for the bitstring to increase in length over time, and whether these characteristics seem plausible.

  72. 72
    LocalMinimum says:

    I’d say we need to pull out all the stops and fully simulate creatures on a full physical basis, and have their features emergent from component aggregates whose members are coded by a code that has a complex semiotic relationship with the expressed components. The whole nine yards, no expense spared.

    But, if we were right, and Darwin were wrong, and it didn’t do anything…Who would pay for our “broken” simulation?

  73. 73
    Eugene S says:

    Seversky

    “Naturalistic/materialist/physicalist accounts of the observable world have been found to work very well, in the case of quantum theory, to a very high degree of precision. All the modern technology we take for granted bears witness to that.”

    Intelligibility of this world bears witness to this entire world having been created by an intelligence. All the modern technology we take for granted bears witness to that.

    The success of the application of the scientific method that produced modern technology has nothing to do with materialism. In the same way, evolution as an idea does not have any bearing on the actual success of biotechnology. Biotechnology does not invoke evolution at all, as the late Prof P. Skell pointed out. Evolution is put in white papers post-factum for ideological purposes. Intelligent guidance, which is used in technology, is the opposite of evolution, conceptually.

  74. 74
    groovamos says:

    Allan Keth: By that definition, there is little doubt that information is found in living organisms. But, using the same definition, it is also found in inanimate matter.

    NO – I’ve said it many times on here, information requires the context of mind. Suppose we were to measure the distance between the nucleii of two atoms on a rock at absolute zero temperature. How much self-information is in a single measurement (estimator)? It is dependent on the measurement method and actual scalar value of the distance. The method is characterised with a Gaussian error distribution. How would we determine the actual scalar value? We would have to take a huge number of measurements using an unbiased method, approaching infinity, to determine an expected value. As the number of measurements increases, so does the self-information of the expected value, and we would determine the estimator standard deviation. So with the standard deviation and the expected value we can calculate the self-information of a single measurement. In this way you can see that the distance between two atoms has no self-information; only our activities to determine that distance comprise self-information. The self information of our determination has no upper bound, it is limited only by the number of measurements we are willing to make.

  75. 75
    kairosfocus says:

    JDK,

    The issue is not Lewontin as such but the views, agendas and tactics of the secularist elites he so vividly (and largely inadvertently) exposed.

    And indeed, the pattern of behaviours we see again and again underscores the point.

    KF

    PS: Note the pattern as highlighted:

    . . . to put a correct [–> Just who here presume to cornering the market on truth and so demand authority to impose?] view of the universe into people’s heads

    [==> as in, “we” the radically secularist elites have cornered the market on truth, warrant and knowledge, making “our” “consensus” the yardstick of truth . . . where of course “view” is patently short for WORLDVIEW . . . and linked cultural agenda . . . ]

    we must first get an incorrect view out [–> as in, if you disagree with “us” of the secularist elite you are wrong, irrational and so dangerous you must be stopped, even at the price of manipulative indoctrination of hoi polloi] . . . the problem is to get them [= hoi polloi] to reject irrational and supernatural explanations of the world [–> “explanations of the world” is yet another synonym for WORLDVIEWS; the despised “demon[ic]” “supernatural” being of course an index of animus towards ethical theism and particularly the Judaeo-Christian faith tradition], the demons that exist only in their imaginations,

    [ –> as in, to think in terms of ethical theism is to be delusional, justifying “our” elitist and establishment-controlling interventions of power to “fix” the widespread mental disease]

    and to accept a social and intellectual apparatus, Science, as the only begetter of truth

    [–> NB: this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]

    . . . . To Sagan, as to all but a few other scientists [–> “we” are the dominant elites], it is self-evident

    [–> actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . . and in fact it is evolutionary materialism that is readily shown to be self-refuting]

    that the practices of science provide the surest method of putting us in contact with physical reality [–> = all of reality to the evolutionary materialist], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [–> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . .

    It is not that the methods and institutions of science somehow compel us [= the evo-mat establishment] to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [–> irreconcilable hostility to ethical theism, already caricatured as believing delusionally in imaginary demons]. [Lewontin, Billions and billions of Demons, NYRB Jan 1997,cf. here. And, if you imagine this is “quote-mined” I invite you to read the fuller annotated citation here.]

  76. 76
    Eric Anderson says:

    AK:

    By that definition, there is little doubt that information is found in living organisms. But, using the same definition, it is also found in inanimate matter.

    Are you really arguing that there is no difference in information content between DNA and something like, say, a flurry of sand scattered by the wind or an asteroid hurtling through space? Is that really your argument?

    If not, then please take a moment to describe the difference.

    —–

    (Hint: Physical objects do not contain information by their mere existence.)

  77. 77
    jdk says:

    Given kf’s constant posting of his highly editorialized quote from Lewontin, I decided to look at the original. which comes from a long article about Carl Sagan in the New York Review of Books in 1997. For those of you interested, here are the three key paragraphs.

    With great perception, Sagan sees that there is an impediment to the popular credibility of scientific claims about the world, an impediment that is almost invisible to most scientists. Many of the most fundamental claims of science are against common sense and seem absurd on their face. Do physicists really expect me to accept without serious qualms that the pungent cheese that I had for lunch is really made up of tiny, tasteless, odorless, colorless packets of energy with nothing but empty space between them? Astronomers tell us without apparent embarrassment that they can see stellar events that occurred millions of years ago, whereas we all know that we see things as they happen. When, at the time of the moon landing, a woman in rural Texas was interviewed about the event, she very sensibly refused to believe that the television pictures she had seen had come all the way from the moon, on the grounds that with her antenna she couldn’t even get Dallas. What seems absurd depends on one’s prejudice. Carl Sagan accepts, as I do, the duality of light, which is at the same time wave and particle, but he thinks that the consubstantiality of Father, Son, and Holy Ghost puts the mystery of the Holy Trinity “in deep trouble.” Two’s company, but three’s a crowd.

    Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.

    The mutual exclusion of the material and the demonic has not been true of all cultures and all times. In the great Chinese epic Journey to the West, demons are an alternative form of life, responsible to certain deities, devoted to making trouble for ordinary people, but severely limited. They can be captured, imprisoned, and even killed by someone with superior magic.6 In our own intellectual history, the definitive displacement of divine powers by purely material causes has been a relatively recent changeover, and that icon of modern science, Newton, was at the cusp. It is a cliché of intellectual history that Newton attempted to accommodate God by postulating Him as the Prime Mover Who, having established the mechanical laws and set the whole universe in motion, withdrew from further intervention, leaving it to people like Newton to reveal His plan. But what we might call “Newton’s Ploy” did not really get him off the hook. He understood that a defect of his system of mechanics was the lack of any equilibrating force that would return the solar system to its regular set of orbits if there were any slight perturbation. He was therefore forced, although reluctantly, to assume that God intervened from time to time to set things right again. It remained for Laplace, a century later, to produce a mechanics that predicted the stability of the planetary orbits, allowing him the hauteur of his famous reply to Napoleon. When the Emperor observed that there was, in the whole of the Mécanique Céleste, no mention of the author of the universe, he replied, “Sire, I have no need of that hypothesis.” One can almost hear a stress on the “I.

  78. 78
    bornagain77 says:

    Eric Anderson, methinks that AK is being, #1, purposely obtuse about information, and #2, he doesn’t really know the first thing about information.

    Information is physical (but not how Rolf Landauer meant) – video
    https://youtu.be/H35I83y5Uro

    Information engine operates with nearly perfect efficiency – Lisa Zyga – January 19, 2018
    Excerpt: Physicists have experimentally demonstrated an information engine—a device that converts information into work—with an efficiency that exceeds the conventional second law of thermodynamics. Instead, the engine’s efficiency is bounded by a recently proposed generalized second law of thermodynamics, and it is the first information engine to approach this new bound.,,,
    https://phys.org/news/2018-01-efficiency.html

    What is information? – animated video (May 2016)
    Quote: “If information is not (physically) real then neither are we”
    https://www.youtube.com/watch?v=2AvIOzVJMCM

    Although the preceding is certainly very strong evidence for the physical reality of immaterial information, the coup de grace for demonstrating that immaterial information is its own distinct physical entity, separate from matter and energy, is Quantum Teleportation:

    Quantum Teleportation Enters the Real World – September 19, 2016
    Excerpt: Two separate teams of scientists have taken quantum teleportation from the lab into the real world.
    Researchers working in Calgary, Canada and Hefei, China, used existing fiber optics networks to transmit small units of information across cities via quantum entanglement — Einstein’s “spooky action at a distance.”,,,
    This isn’t teleportation in the “Star Trek” sense — the photons aren’t disappearing from one place and appearing in another. Instead, it’s the information that’s being teleported through quantum entanglement.,,,
    ,,, it is only the information that gets teleported from one place to another.
    http://blogs.discovermagazine......-HqWNEoDtR

  79. 79
    Allan Keith says:

    ET,

    Everything, apparently. Information only comes from intelligence, ie a mind.

    Has this been proven? I would love to see the papers.

    The specific arrangements of information that is required to produce living organisms only comes from intelligence.

    Has this been proven? I would love to see the papers.

    The specific arrangements of information to produce the laws of physics and chemistry only comes from intelligence.

    Has this been proven? I would love to see the papers.

    LocalMinimum,

    Information denial is not really an option for an A/Mat who isn’t operating on blind faith.

    I am not denying the existence of information. It is found everywhere, as you indicated. What is in question is whether it can only be the result of an intelligence.

    EricMH,

    Anyways, the point is that evolution is easy to simulate on a computer, at much greater timescales than in the history of our world. Even then, it just doesn’t do that much. If species did evolve, it is not thanks to evolution, but thanks to incredible amounts of built in pathways in the search landscape.

    I think that you are greatly oversimplifying the complexities involved. Billions of organisms, over billions of years, with billions of random mutations, and billions of environmental impacts, and billions of…. I think that you get the idea. But what I find ironic is that the same people who claim that AGM is most likely false because the system is too complex to properly model, claim that the models prove that evolution is false, even though the variables involved are every bit as complex, if not more complex, than weather patters and climate.

    Groovamos,

    NO – I’ve said it many times on here, information requires the context of mind.

    A qualified agreement. Stable isotope ratios carry information, tree rings in temperate zones carry information, a water molecule carries information, DNA carries information, RNA carries information. But only if there is something around to interpret/read the information. Humans do that quite nicely. As, I would argue, do most other organisms, although probably a different way.

    Eric,

    Hint: Physical objects do not contain information by their mere existence.

    I agree. They need something to interpret/read it. To an amoeba, a chemical gradient carries information that the amoeba can ‘read’. To us, the same chemical gradient would also carry information, but nobody is suggesting that the way we ‘read’ this information, or what information we glean from it, are the same as the way an amoeba ‘reads’ the information.

  80. 80
    Eric Anderson says:

    AK:

    There are some pretty critical nuances that will be helpful if you are sincerely interested in understanding information (many ID proponents could also take a lesson here):

    1. There is a difference between information and communication. Don’t conflate the two. This is an incredibly common mistake.

    2. Information can exist even if there is no receiver to receive it and do something with it. Indeed, the information must exist before it is received, otherwise there is nothing to receive (or send in the first place, for that matter).

    3. There is a difference between the mere existence of a physical object and information being contained in, or if we prefer, represented by a physical object.

    4. It is possible to have a system that reacts to a certain physical object (or electrochemical differential, such as your chemical gradient example). That does not mean that the physical object contains information in and of itself.

    5. Your use of the word “read” is a conflation and muddies the water. There is a difference between truly reading information represented by an object and identifying physical characteristics of an object.

    6. Information represents something outside of itself. A rock hurtling through space or a chemical gradient doesn’t represent anything outside of itself.

    —–

    All of this is very fundamental to any proper understanding of information. If you think a chemical gradient is in the same category as the contingent, specific arrangement of nucleotides in DNA, that is a serious category error.

    I hope you aren’t under that mis-impression. That is why I requested that you describe the difference in information content between DNA and, say, a rock hurtling through space.

    I repeat the request. If you can accurately articulate the difference then I’ll know there is an understanding of the basics and that there may be value in continuing the discussion.

  81. 81
    ET says:

    Allan Keith:

    Has this been proven?

    Yes, as much as anything in science. No one has ever observed blind and mindless processes producing information and every observation and experience demonstrates information only comes from intelligence.

    Billions of organisms, over billions of years, with billions of random mutations, and billions of environmental impacts, and billions of

    Where did you get those organisms from? Amazon? And how do you know there was billions of years? The age of the earth depends on how it was formed. And seeing that no one knows then the age is just a guess based on untestable assumptions.

  82. 82
    kairosfocus says:

    JDK, the fuller cite indeed the whole article is linked from my annotated clip. It further underscores my point. KF

    PS: Let me clip:

    >>Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural.>>

    Notice, the strawmannish opposition and equivalence of science as a materialistic ideology

    >> We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism.>>

    Ideology

    >> It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.>>

    Ditto

    >> The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything.>>

    Nonsense

    >> To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen>>

    Theism stands on the God of order who may act beyond that order relatively rarely for good cause. and were the cosmos a chaos, no sign could stand out. Miracles require an intelligibly orderly world, amenable to science.

  83. 83
    Eric Anderson says:

    Seversky @31:

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock. In my view, it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    Almost, but not quite.

    Surely you aren’t arguing that there is no substantive difference between DNA and a rock in regards to information?

    Surely you aren’t suggesting that if only we were to turn our “modeling languages and simluations” to examining a piece of rock that we would discover something similar to what has been found in DNA?

    You are almost on the right track. We should not confuse the physical characteristics of a piece of rock with the information we produce as intelligent beings when we examine the piece of rock. That is a very important point I have been harping on for years.

    But to reject the idea that a physical object can be a medium for real information is absurd. We have many examples of such, including the very screen you are looking at. So you are almost on the right track. The problem is that you seem intent on denying the obvious information contained in DNA, and so you mistakenly throw it under the bus along with the piece of rock.

    There is a world of difference between DNA and a piece of rock, as everyone from Crick to a school child knows. Let’s have the courage to address head on the question of where the information in DNA came from, instead of patently absurd attempts to deflect the issue by sloppy definitions and embarrassing attempts to deny the existence of the information that everyone knows is there.

  84. 84
    kairosfocus says:

    PPS: I trust the legitimacy, relevance and utility of a markup stands illustrated.

  85. 85
    Eric Anderson says:

    Let us also observe that the information contained in DNA did not arise due to our models and simulations. It was discovered. Then we build models and simulations and tools of analysis to help us better understand it. Any models or simulations or analyses of genetic information are based on what is actually in DNA, not the other way around. Any contrary suggestion is completely backwards.

  86. 86
    jdk says:

    kf writes, “The fuller cite indeed the whole article is linked from my annotated clip.”

    True, but I was glad to read the whole context, as your chopped up, editorialized version is not very useful.

    kf writes, “It further underscores my point.”

    That is a matter of opinion. Lewontin seems to be quite a bit more nuanced than your summary seems to show.

    And let me make it clear: I am not a committed materialist, as Lewontin and Sagan are, and I certainly don’t believe science is the only “begetter of truth.” I’m not posting here to defend every word of Lewontin’s: I just thought it was useful to get the non-kf’ed version.

  87. 87
    EricMH says:

    @Bob O’H, after a bit of thought it’s easy to incorporate beneficial mutations into the model. We just add a new probability that a mutation is beneficial.

    So, with the original model, where survival is modeled by probability of no mutations, where p is mutation probability per bit and L is length of organism’s genome:

    s = (1-p)^L

    we add q to be the probability a mutation is harmful:

    s = (1-pq)^L

    Now, we want to know how q changes as L grows and s remains constant, so we solve for q:

    q = (1-s^(1/L))/p

    As L approaches infinity (oo) q becomes 0:

    q = (1-s^(1/oo))/p = (1-s^0)/p = (1-1)/p = 0/p = 0

    The upshot of this equation is that as the organism’s genome grows, the probability a mutation is beneficial approaches 1. So, with our enormous genome, we should be able to walk through a nuclear reactor and come out the other end with super powers. I guess this is the rationale behind Ninja Turtles and X-Men.

  88. 88
    EricMH says:

    For those who disregard mathematical models of physical phenomena as not telling us anything useful, what is your opinion of f=ma? On the other side, because I am quite skeptical of global warming, a model is only as good as its assumptions. Plus, their models are super complex. The simpler a model, the better, per Occam’s razor.

  89. 89
    jdk says:

    Eric writes,

    “The simpler a model, the better, per Occam’s razor.”

    Extremely wrong! And not what Occam’s razor says!

  90. 90
    kairosfocus says:

    JDK, what he said speaks for itself, as I highlighted. I did not make it up: the gross blunder of scientism where a phil view is asserted that undermines phil views. The telling metaphor that literally demonises theism. The open contempt to theists (notice the example of a woman who does not understand how a video signal could get here from the Moon — the man who got us to the Moon had become a Christian). The a priori materialism. The insinuation of irrationality as the hallmark of theism. Utter failure to know that as miracles are signs, a world in which miracles happen and are recognisable has to be one that is an orderly cosmos not an utterly unintelligible chaos. The link between this and the origin of modern science, and more. Where, there is serious evidence that this sort of contempt is far more common than any responsible person would be comfortable with. The enthusiasm greeting Dawkins et al on so-called new atheism in some quarters speaks, tellingly. KF

  91. 91
    EricMH says:

    @jdk Extremely right. Exactly what Solomonoff proved with Solomonoff induction, and is the basis of all machine learning and statistical methods.

    “Everything should be made as simple as possible, but not simpler.”
    – Albert Einstein (attributed)

  92. 92
    kairosfocus says:

    JDK & EMH, simplicity is different from being simplistic, indeed — what is unrealistically simplified to the point of material error is not a good model. Einstein was credited with things should be as simple as possible but not simpler than that. KF

  93. 93
    Bob O'H says:

    Eric @ 87 – I don’t know about you, but I don’t have an infinite genome.

    You should have a look at the Basener & Sanford paper, they do a better job (even if I don’t like aspects of their model).

  94. 94
    Allan Keith says:

    EricMH,

    The simpler a model, the better, per Occam’s razor.

    I think that you have to qualify this. The simpler the model that accurately models the observations, the better.

    I don’t think that anyone is suggesting that you can accurately model evolution by only including DNA, random mutations and selection.

  95. 95
    EricMH says:

    @Bob O’H, the point is mutations must become less harmful as the genome becomes longer in order to maintain a constant survival rate. Counter intuitive to me, at least.

    @AK, yes, that is correct. The model must also be accurate, otherwise the simplest model is no model. However, accuracy alone is insufficient, because the most accurate model is always the data itself. What we need is a model that is both accurate and parsimonious. There is also a tradeoff, where we can trade a bit of accuracy for a much simpler model. This is the case with physics formulae, such as f=ma, which are extremely simple, but cannot be 100% accurate due to quantum effects.

  96. 96
    jdk says:

    So how do you propose to test your model, Eric to see if it is accurate? Are you modeling a particular genome such that you can compare your simulation with what happens in the real world?

    If not, how do you know that your simulation is a relatively accurate model?

    That is why I said that your saying “the simpler the model the better” was wrong. If a model must be complex in order to be testably accurate, then so be it. The key thing is to accurately reflect reality in ways that can be empirically tested.

  97. 97
    EricMH says:

    @JDK, I’m not claiming my model resembles biological reality. I’m claiming my model captures everything in the Darwinian concept of evolution. If my model does not match reality, then neither does Darwinian evolution.

  98. 98
    bornagain77 says:

    In discussions about information on UD, 99% of the talk on UD about information comes down to, basically, the sheer impossibility of blind searches to find functional sequences in sequence space. This is all fine and well as far it goes, (since it shows Darwinian mechanisms to be grossly inadequate for the task at hand), but I hold that these usual discussions about information on UD completely miss the bigger picture about information. Namely, that immaterial information is now shown experimentally to be its own distinct physical entity that is separate, and independent, from matter and energy. And more specifically, since this distinct physical entity of immaterial information exists separately, and independently, from matter and energy, then any reductive materialistic (i.e. Darwinian) explanations which claim information is merely a “metaphor”, or which claim that information is merely ’emergent’ from a material basis, are falsified empirically with direct physical evidence.
    That is to say, the fact that immaterial information is now shown experimentally to be a physically real entity that is separate, and independent, from matter and energy changes the entire debate from an argument about whether unguided material processes can ever possibly generate functional information or not, to an empirical observation that immaterial information will never be reducible to any possible reductive materialistic (i.e. Darwinian) explanation, period.

    In the following paper, Prof. Andy C. McIntosh, who is professor of thermodynamics and combustion theory at the University of Leeds, holds that it is non-material information that constrains biological life to be so far out of thermodynamic equilibrium. Moreover, Dr. McIntosh holds that regarding information as independent of energy and matter ‘resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions’.

    Information and Thermodynamics in Living Systems – Andy C. McIntosh – 2013
    Excerpt: ,,, information is in fact non-material and that the coded information systems (such as, but not restricted to the coding of DNA in all living systems) is not defined at all by the biochemistry or physics of the molecules used to store the data. Rather than matter and energy defining the information sitting on the polymers of life, this approach posits that the reverse is in fact the case. Information has its definition outside the matter and energy on which it sits, and furthermore constrains it to operate in a highly non-equilibrium thermodynamic environment. This proposal resolves the thermodynamic issues and invokes the correct paradigm for understanding the vital area of thermodynamic/organisational interactions, which despite the efforts from alternative paradigms has not given a satisfactory explanation of the way information in systems operates.,,,
    http://www.worldscientific.com.....08728_0008

    And in support of Dr. McIntosh’s contention that it must be non-material information which constrains biological life to be so far out of thermodynamic equilibrium, information has now been experimentally shown to have a ‘thermodynamic content’:

    And in support of Dr. McIntosh’s contention that it must be non-material information which constrains biological life to be so far out of thermodynamic equilibrium, information has now been experimentally shown to have a ‘thermodynamic content’:

    Demonic device converts information to energy – 2010
    Excerpt: “This is a beautiful experimental demonstration that information has a thermodynamic content,” says Christopher Jarzynski, a statistical chemist at the University of Maryland in College Park. In 1997, Jarzynski formulated an equation to define the amount of energy that could theoretically be converted from a unit of information2; the work by Sano and his team has now confirmed this equation. “This tells us something new about how the laws of thermodynamics work on the microscopic scale,” says Jarzynski.
    http://www.scientificamerican......rts-inform

    This work has now been extended:

    New Scientist astounds: Information is physical – May 13, 2016
    Excerpt: Recently came the most startling demonstration yet: a tiny machine powered purely by information, which chilled metal through the power of its knowledge. This seemingly magical device could put us on the road to new, more efficient nanoscale machines, a better understanding of the workings of life, and a more complete picture of perhaps our most fundamental theory of the physical world.
    http://www.uncommondescent.com.....-physical/

    Information engine operates with nearly perfect efficiency – Lisa Zyga – January 19, 2018  
    Excerpt: Physicists have experimentally demonstrated an information engine—a device that converts information into work—with an efficiency that exceeds the conventional second law of thermodynamics. Instead, the engine’s efficiency is bounded by a recently proposed generalized second law of thermodynamics, and it is the first information engine to approach this new bound.,,,
    https://phys.org/news/2018-01-efficiency.html

    Of related note to immaterial information having a ‘thermodynamic content’, classical digital information was found to be a subset of ‘non-local’, (i.e. beyond space and time), quantum entanglement/information by the following method which removed heat from a computer by the deletion of data:

    Quantum knowledge cools computers: New understanding of entropy – June 2011
    Excerpt: No heat, even a cooling effect;
    In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.”
    http://www.sciencedaily.com/re.....134300.htm

    And in direct contradiction to Landauer’s (and Darwinian) contentions that immaterial information does not exist independent of matter and energy, Dr Vaccaro states in regard to the preceding thought experiment that “Landauer said that information is physical because it takes energy to erase it. We are saying that the reason it (information) is physical has a broader context than that.”,

    Scientists show how to erase information without using energy – January 2011
    Excerpt: Until now, scientists have thought that the process of erasing information requires energy. But a new study shows that, theoretically, information can be erased without using any energy at all.,,, “Landauer said that information is physical because it takes energy to erase it. We are saying that the reason it (information) is physical has a broader context than that.”, Vaccaro explained.
    http://www.physorg.com/news/20.....nergy.html

    Although the preceding is certainly very strong evidence for the physical reality of immaterial information, the coup de grace for demonstrating that immaterial information is its own distinct physical entity, separate from matter and energy, is Quantum Teleportation:

    Quantum Teleportation Enters the Real World – September 19, 2016
    Excerpt: Two separate teams of scientists have taken quantum teleportation from the lab into the real world.
    Researchers working in Calgary, Canada and Hefei, China, used existing fiber optics networks to transmit small units of information across cities via quantum entanglement — Einstein’s “spooky action at a distance.”,,,
    This isn’t teleportation in the “Star Trek” sense — the photons aren’t disappearing from one place and appearing in another. Instead, it’s the information that’s being teleported through quantum entanglement.,,,
    ,,, it is only the information that gets teleported from one place to another.
    http://blogs.discovermagazine......-HqWNEoDtR

    Moreover, this physically real quantum information which is shown to have, contrary to Landauer’s (and Darwinian) assertions, an existence that is separate from matter and energy, is also found to be ‘conserved’. That is to say, ‘the conservation of quantum information means that information cannot be created nor destroyed.’

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment.
    http://www.physorg.com/news/20.....tally.html

    This physically real quantum information can perform a number of tasks that are impossible for classical information. Impossible tasks which provide the motivation to build quantum computers.

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

  99. 99
    bornagain77 says:

    As well this physically real quantum information, which cannot be created or destroyed, is also now found in molecular biology on a massive scale. In every DNA and protein molecule:

    “What happens is this classical information (of DNA) is embedded, sandwiched, into the quantum information (of DNA). And most likely this classical information is never accessed because it is inside all the quantum information. You can only access the quantum information or the electron clouds and the protons. So mathematically you can describe that as a quantum/classical state.”
    Elisabeth Rieper – Classical and Quantum Information in DNA – video (Longitudinal Quantum Information resides along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”
    https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

    Moreover, this Quantum Information in molecular biology, since it can perform computational tasks that are impossible for classical information, provides coherent solutions for the protein folding enigma, DNA search problems, and for exactly why life is so far out of thermodynamic equilibrium in the first place.

    Darwinian Materialism vs Quantum Biology – video
    https://www.youtube.com/watch?v=LHdD2Am1g5Y

    Besides providing direct empirical falsification of Landauer’s claim, and neo-Darwinian claims in general, claims that say immaterial information does not exist apart from its representation on a physical medium, the implication of finding ‘non-local’, beyond space and time, and ‘conserved’, quantum information in molecular biology on such a massive scale, in every DNA and protein molecule, is fairly, and pleasantly, obvious.
    That pleasant implication, or course, being the fact that we now have very strong physical evidence directly implying that we do indeed have an eternal soul that lives beyond the death of our material bodies.
    In the following video Stuart Hameroff states ‘it’s possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”

    “Let’s say the heart stops beating. The blood stops flowing. The microtubules lose their quantum state. But the quantum information, which is in the microtubules, isn’t destroyed. It can’t be destroyed. It just distributes and dissipates to the universe at large. If a patient is resuscitated, revived, this quantum information can go back into the microtubules and the patient says, “I had a near death experience. I saw a white light. I saw a tunnel. I saw my dead relatives.,,” Now if they’re not revived and the patient dies, then it’s possible that this quantum information can exist outside the body. Perhaps indefinitely as a soul.”   
    – Stuart Hameroff – Quantum Entangled Consciousness – Life After Death – video (5:00 minute mark)
    https://youtu.be/jjpEc98o_Oo?t=300

  100. 100
    EricMH says:

    @BA77, thanks for this information. I agree that information has been shown to be something distinct, but there are some nuances that are missed. Information itself is inert, it cannot produce more information. If information exists, then an information creator must also exist. However, since information is inert, then the creator cannot itself be information but something other. Thus, our pantheon of basic substances must expand to not only include information but also this fourth entity that can create information.

    My personal hypothesis is the human soul is of this fourth variety. Notice that by this formulation the human soul cannot itself be derived from matter (chance + necessity + information), and consequently the dissolution of matter does not entail the dissolution of the soul.

  101. 101
    Allan Keith says:

    EricMH,

    My personal hypothesis is the human soul is of this fourth variety. Notice that by this formulation the human soul cannot itself be derived from matter (chance + necessity + information), and consequently the dissolution of matter does not entail the dissolution of the soul.

    Eric, thank you for your honesty. But let’s take a hypothetical. Let’s assume that humans never existed. Without humans, are there souls? Is there ID? Is there information?

  102. 102
    EricMH says:

    @AK I guess there could be souls. Depends what other beings populate your hypothetical universe. But, if there are no souls, there is no ID and there is no information. The chain of being starts with souls and ends in necessity, where latter elements cannot come from prior elements.

    Actually, if souls exist, there must also be a 5th entity, a soul creator, which we cannot be since we cannot create ourselves. Now, you might think this chain goes on forever, but we can simply say the 5th entity is self existent. An infinite regress is not possible, and since it must terminate somewhere, it might as well terminate with the 5th.

  103. 103
    bornagain77 says:

    EricMH, I did not extend the argument from immaterial information that far, i.e. to the Creator, but of course that conclusion, i.e. a transcendent Creator of immaterial information, necessarily follows. I was merely pointing out the fact that Darwinian, i.e. reductive materialistic, explanations for immaterial information, as far as the empirical science itself is now concerned, are now falsified.

    That in itself is certainly not a minor point.

  104. 104
    Allan Keith says:

    EricMH,

    AK I guess there could be souls. Depends what other beings populate your hypothetical universe.

    I am just talking about an earth without humans. I think that we would agree that the earth, and other life forms, would get along quite happily without us. We really don’t bring much to the table that benefits them. Other that cats, dogs, rats and bed bugs.

    But, if there are no souls, there is no ID and there is no information.

    Finally. Some brutal honesty. So, without souls, there is no ID and no information. Is there life? Do bacteria rely on our souls? Amaebae? Paramecia? Dung beetles? What I am trying to say is that life on earth is not contingent on our existence. In fact, it might be hindered by it. What purpose do we serve in the biosphere?

  105. 105
    EricMH says:

    @AK, we may be talking past each other here. Without information there is no universe, biosphere, etc. Something soul like has to have created all the information that gives our universe its form.

    The question of animals, and life in general, is a bit more difficult. I’m just giving out my personal opinion here. I believe in a sort of vitalism, that life itself cannot be reduced to chance and necessity, and exhibits teleology. Now what differentiates life in general from intelligent agency is an even deeper question. My thought is that intelligent agency can choose between ends, whereas life is directed towards one end.

    Anyways, all of this gets deep into the philosophical weeds. The chain of being: matter, information, soul, meta-soul, is what is deductively clear from the math and evidence we have.

  106. 106
    Seversky says:

    Everyone’s talking glibly about information as if it is some neat unitary entity which we all understand and agree on. So are we talking about Kolmogorov information or Shannon information or Fisher information or Jack Szostak’s functional information? Back on Oct 9 2009, William Dembski noted in an OP that Professor Seth Lloyd had cataloged upwards of forty different version of information or complexity measures in use in various disciplines. Even allowing for some duplication that’s a serious potential for misunderstanding or equivocation. So talking about everything being made of information is about as helpful as saying everything is made of luminiferous ether.

  107. 107
    Eric Anderson says:

    Seversky @106:

    You have a point — to an extent.

    But let’s not avoid the issues on the table with a rhetorical deflection, pointing out that there might be possible definitional issues.

    The standard, ordinary, everyday usage of the word is plenty adequate for the key issues on the table — both on this thread and for intelligent design generally. We don’t need some be-all-and-end-all definition that everyone agrees on before we can start asking some fundamental questions.

    Specifically, the points I made at 83 (and 85) are perfectly reasonable, understandable and answerable. What are your answers?

    So talking about everything being made of information is about as helpful as saying everything is made of luminiferous ether.

    I agree that talking about “everything being made of information” isn’t helpful. It isn’t even meaningful, in my opinion. Not because there are lots of reasonable different definitions of information. But because it isn’t true in any meaningful or useful sense.

    —–

    Incidentally, many of the supposedly differing types of “information” (Kolmogorov, Shannon, etc.) are just the result of sloppy terminology and shallow thinking. For example, when we really understand what so-called “Shannon information” is, we understand that we aren’t dealing with some special kind of information that needs to be treated in its own special way, but just ordinary, everyday, run-of-the-mill information that happens to inform us about a particular measurement. Pox on the person who first started using the unhelpful term “Shannon information” . . .

    Szostak’s “functional information” also leads us right back to the good old-fashioned, everyday concept of information. So despite various fancy terms, in most cases all we are dealing with is a particular application of information or a particular instantiation of information, not some separate type of information we need to wring our hands over, or spend a lot of time agreeing upon, or handle according to special rules.

  108. 108
    gpuccio says:

    Seversky:

    In all ID reasonings, it’s definitely functional information: the complexity necessary to implement a function.

    No possible equivocations about that.

  109. 109
    Origenes says:

    As GPuccio points out we are talking about functional information. Why is this so hard to find for raw chemistry? Foremost, because chemistry is not at all interested in function. If organisms are nothing but chemistry, then there is no function. The function of the cat’s eyes is relative to the cat. Replace ‘the cat’ with ‘chemistry’ and the sentence no longer makes sense. Without the cat there is nothing for the eyes to serve — to be ‘functional for’.
    The same goes for reason and truth. Why is it hard to believe that neuronal chemistry comes up with the truth? The same reason: chemistry is not at all interested in truth.

  110. 110
    ET says:

    Seversky:

    Everyone’s talking glibly about information as if it is some neat unitary entity which we all understand and agree on.

    Yes, buy a dictionary. According to Meyer in “Signature in the Cell” the following in the definition to use:

    b : the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (such as nucleotides in DNA or binary digits in a computer program) that produce specific effects

    Shannon told us how to measure it.

  111. 111
    ET says:

    Eric Anderson:

    I agree that talking about “everything being made of information” isn’t helpful.

    I disagree. It is always helpful to say what something is made up of. Shannon’s isn’t a type of information. It is a way to measure information.

  112. 112
    ET says:

    EricMH:

    But, if there are no souls, there is no ID and there is no information.

    What? Please show your work.

    Since when does ID rely on souls?

  113. 113
    ET says:

    Allan Keith:

    Let’s assume that humans never existed. Without humans, are there souls? Is there ID? Is there information?

    1- It doesn’t matter

    2- ID doesn’t depend on humans

    3- ID does not depend on souls

    4- Yes, there would be information- if something existed

  114. 114
    Bob O'H says:

    Origenes @ 109 – we know the biochemistry of E. coli, for example, and as far as I know it’s all to do with chemistry. This includes DNA replication and gene expression. So if the biology of E. coli reduces down to chemistry, does that mean that it has no function?

  115. 115
    ET says:

    Bob- If DNA replication and gene expression were purely chemical processes then it should be easy to create that in a test tube. Yet we cannot.

  116. 116
    Eugene S says:

    Bob O’H

    Does the game of chess reduce to chemistry? I.e. Does the rule prescribing how a knight or a queen should move on the board reduce to chemistry?

  117. 117
    Bob O'H says:

    ET @ 115 – we’ve been able to do both of those for a few decades.

    Eugene S – let’s not get sidetracked.

  118. 118
    gpuccio says:

    Bob O’H:

    I think you understand perfectly that the point is the functional configuration of the biological matter.

    Of course biological objects work (mainly) at the level of biochemistry. Like objects in a computer work by electromagnetic laws.

    And of course whar really matters is the configuration. Both for biological objects (configuration of nucleotides, of AAs, of mpolecules, and so on) and for a computer (configuration of semiconductors, of connections, and so on).

    Configuration is everything for function. In any machine, it’s configuration which is related to function, not the laws of mechanics or of electromagmetism or of biochemistry. Those laws are just the substrate where configuration is imprinted to achieve function. That is the functional information.

    But, of course, you are intelligent enough to understand all that very well. So, why play games?

  119. 119
    ET says:

    Bob:

    we’ve been able to do both of those for a few decades.

    Reference please.

  120. 120
    gpuccio says:

    Bob O’H:

    “ET @ 115 – we’ve been able to do both of those for a few decades.”

    Yes. But using the information in existing molecules, not certainly designing it ourselves.

    It’s like saying that we are capable of writing Shakespeare’s sonnets only because we can easily print them from our computer.

    Again, why play games?

  121. 121
    Eugene S says:

    Bob,

    I was not getting sidetracked! That is the real issue here. Unfortunately, your response 117 is a marker of a lack of understanding that the genetic translation apparatus, exactly like chess, is a semiotic state system.

    Semiosis is sign processing. Sign is a category complementary to matter. Sings themselves are material (chemical if you like) of course. However, from a physics perspective, their role in a semiotic system is to provide symbolic boundary conditions on (=organize) the motion of matter.

    That there is a formal correspondence (cf a rule how a queen should move on the chessboard) between aminoacids and codons, cannot be reduced to chemistry. The genetic code is code in the same strict sense, as a text in English or Spanish is code.

  122. 122
    gpuccio says:

    ET:

    It’s easy enough, I believe, to do those things in a cell free system using existing molecules and components. At least, protein synthesis can certainly be easily achieved that way.

    See here:

    https://en.wikipedia.org/wiki/Cell-free_system

  123. 123
    gpuccio says:

    Eugene S:

    Yes, but it’s not only the semiosis. The code is important, but the functional information that is written by the code is very important too.

    So, a Shakespeare’s sonnet is amazing for both things: the code (English language) and its functional information (the content of the sonnet).

    So, a protein coding gene is amazing for both things: the code (the genetic code) and its functional information (the sequence of nucleotides to be translated into the functional sequence of AAs).

    Moreover, while the information in the code is shared by all protein coding genes, the information for each protein is unique, or however specific.

    Neither the code nor the functional information depend, in any way, from the chemistry which allows protein synthesis. Of course, they need that chemistry to work, but that is all another concept.

  124. 124
    ET says:

    gpuccio, Thank you. So these cell-free systems act as if they are normal cells? It seems to me that the scientists still have to do some manipulating to get things accomplished.

  125. 125
    Bob O'H says:

    ET @ 119 – For DNA replication, look up PCR. For in vitro gene expression, there are plenty of references on Google Scholar.

  126. 126
    Bob O'H says:

    GPuccio @ 118 –

    I think you understand perfectly that the point is the functional configuration of the biological matter.

    Indeed, but that’s still a part of the chemistry. So, in that sense, where is the information?

    I guess my point is that information is a concept, that we use to help us understand the world: it’s not objectively out there, rather we interpret the world in terms of information.

    There is no information in the cell, only DNA with bases in order. But it’s sometimes helpful to summarise this as information.

  127. 127
    ET says:

    Bob- PCR is not natural. I was looking for DNA replication to occur as a matter of course as it does in the cell.

  128. 128
    ET says:

    Proof-reading, error-correction, editing and splicing are not reducible to chemistry, Bob. Carrying out the genetic code is not reducible to chemistry.

  129. 129
    tribune7 says:

    Bob

    Indeed, but that’s still a part of the chemistry. So, in that sense, where is the information?

    You can say the same thing regarding Shakespeare. It’s just ink on paper i.e. mere chemistry.

  130. 130
    Eugene S says:

    Bob

    “There is no information in the cell, only DNA with bases in order. But it’s sometimes helpful to summarise this as information.”

    I’m afraid this is not correct.

    Information as a concept, of course, assumes a receiver. It does not have to always assume a sender. E.g. we can interpret sensory signals as information, in which case we indeed are talking about a signal. A signal from a supernova when interpreted tells us about the distance from the object, its size and other things.

    However, there are also messages which assume both a sender and a receiver! There is a huge difference between a signal and a message. A message is an objectively identifiable sequence of signs. This or that particular sequence is specific in the sense that it specifies the result of its processing. It specifies a subspace from a space of physically/chemically alternative states. A message assumes an a-priori protocol (agreement, set of rules) between the sender and the receiver, to help correctly encode and interpret the contents of the message.

    What DNA/RNA contain is a message, not merely a signal. That this is a message is a universally accepted scientific finding. The sender is the parent cell, the receiver is the next generation cell.

    An amazing thing is that humans can intercept and change the message to fix genetic malfunction.

  131. 131
    Eugene S says:

    GP 123

    Yes, of course!

  132. 132
    gpuccio says:

    Bob O’H:

    “There is no information in the cell, only DNA with bases in order. But it’s sometimes helpful to summarise this as information.”

    I don’t understand your point. DNA with bases in order is functional information.

    Bits in order in a soruce code are functional information.

    And functional information is not just something that we use to “summarise” things. If there is not the right sequence in our source code, ourprogram cannot work. If there is not the right sequence in our genes, our porteins cannot work.

    This is mcuh more that “a concept, that we use to help us understand the world”. It’s a concept which changes the world.

    I am really surprised that you make such superficial and obviously wrong points!

  133. 133

    gpuccio @ 132: Bob’s comment is not really surprising when you consider his personal bias toward the a/mat philosophical worldview.

    “Still a man hears what he wants to hear and disregards the rest.”
    Paul Simon (The Boxer, 1970)

  134. 134
  135. 135
    Allan Keith says:

    EricMH@97,

    @JDK, I’m not claiming my model resembles biological reality. I’m claiming my model captures everything in the Darwinian concept of evolution. If my model does not match reality, then neither does Darwinian evolution.

    I’m just curious how you include everything from our current understanding of evolution into this ‘simple’ model. Drift, HGT, epigenetics, sexual selection, meiosis, inversions, geography, time, etc. etc. etc. The people who study all of this can’t agree on the importance of the different aspects of the current theory, only that they all play a role. I don’t see how you can model this without making the model very complex.

  136. 136
    Eric Anderson says:

    ET @111:

    I don’t know if you think “everything is made of information”, so we may not be that far apart. This phrase was used by Seversky, but he was apparently referring to what he felt was being proposed by some of the comments in this thread, maybe by you, perhaps by others.

    In any event, it makes no sense to say that a rock floating through space is “made of information”. Physical objects can of course be used to represent information if arranged in a complex specified way, but physical objects don’t contain information by their mere existence.

    It is always helpful to say what something is made up of.

    Of course. And a rock is made up of various minerals and such. It isn’t made of information. Unless we are proposing some definition of “information” that is quite different from the normal understanding of information. In which case, Seversky’s complaint is spot on.

    Shannon’s isn’t a type of information.

    Correct, it isn’t a type of information.

    It is a way to measure information.

    Not quite. Shannon was primarily interested in communication, not information per se. (See my point #1 @80.) He specifically noted that he was not concerned with whether there was genuine functional information underlying the communication. So the Shannon measure isn’t a measure of information in any meaningful sense. The right way to think of it is as a measure of channel capacity.

  137. 137
    jdk says:

    I agree with AK in 135, and would be interested in having Eric give a narrative description about how his simulation models evolution: what factors are taken into consideration, what parameters are involved, etc. (Maybe he has this written up somewhere, or has already posted it here???)

  138. 138
    Origenes says:

    Bob O’H @114

    Suppose that a reputable scientist would propose the hypothesis that the Mona Lisa was not created by intelligent designer L. Da Vinci, but, instead, by a group of medieval toddlers messing with finger paint.
    Would you reject this hypothesis? I would. Why? Multiple reasons, but perhaps foremost because toddlers are not interested in such a depicting of Mona Lisa. I cannot believe that a group of toddlers with finger paint can be aimed at such a result.
    And so it is with chemistry. On its own, chemistry is not aimed at being an organism. And chemistry is not aimed at reason and truth of any kind.

    Bob O’H: So if the biology of E. coli reduces down to chemistry, does that mean that it has no function?

    Yes. The term function would not have meaning. It only makes sense to speak of function in a hierarchical relationship. The part is functional to the whole. Eyes, heart, legs all have function relative to the organism as a whole. They are subservient to their ‘master’ — the whole. If there is no whole (e.g. no cat), only chemistry, then there is nothing to serve. And the term ‘function’ becomes meaningless.

  139. 139
    ET says:

    Eric Anderson:

    I don’t know if you think “everything is made of information”, so we may not be that far apart.

    What isn’t? What can exist absent information?

    In any event, it makes no sense to say that a rock floating through space is “made of information”.

    It takes information to make the atoms. The universe wouldn’t exist without information. It is a fundamental entity.

  140. 140
    EricMH says:

    The hierarchy of being logically follows from the claim that humans *create* CSI. By information I mean CSI.

  141. 141

    There is no information in the cell

    The choice denial of genetic information. wow

  142. 142
    Allan Keith says:

    Origenes,

    And so it is with chemistry. On its own, chemistry is not aimed at being an organism.

    And carbon is not aimed at being a diamond, and water is not aimed at being a snowflake, yet they are both produced by purely physical/chemical means.

    And chemistry is not aimed at reason and truth of any kind.

    But neither is life. The vast bulk of life today and over the last 3+ billion years has no reasoning capabilities. Suggesting that it is aimed towards reason and truth is a human-centric bias.

  143. 143
    jdk says:

    I just read the narrative of Eric’s “model of evolution, which I quote below. I can’t begin to see how this is a realistic model of evolution.

    # This simulation shows random mutation and
    # selection causes organism complexity to stop
    # increasing. This is because the more complex an
    # organism is, the more likely its genome will
    # become corrupted by mutation and it will cease
    # being able to reproduce.
    #
    # Each organism is represented by a bitstring of
    # length L. L is the organism’s complexity.
    # Each generation, the organism will create two
    # offspring with lengths of L-1 and L+1.
    #
    # Each bit in the organism’s bitstring has
    # probability p of becoming corrupt each
    # generation. Consequently, an organism has a
    # probability of 1-(1-p)**L of becoming corrupt
    # each generation. A corrupt organism cannot
    # reproduce and is eliminated from the population.
    #
    # As the simulation runs you will first see the the
    # maximum length in the population will
    # increase each generation. However, the
    # population hits a plateau beyond which complexity
    # does not increase. This happens because larger
    # organisms become corrupted with a higher
    # probability, and eventually they become too
    # easily corrupted to continue creating larger
    # offspring.

  144. 144
    Origenes says:

    Allan Keith @142

    O: And so it is with chemistry. On its own, chemistry is not aimed at being an organism.

    AK: And carbon is not aimed at being a diamond, and water is not aimed at being a snowflake, yet they are both produced by purely physical/chemical means.

    Strong covalent bonding is what carbon does, so, in that sense, it is aimed at being a diamond.
    Don’t tell me that chemistry is not aimed at doing chemical stuff. That’s nonsense.

    O: And chemistry is not aimed at reason and truth of any kind.

    AK: But neither is life.

    Huh? What do you mean with “life”? From your perspective, what else can you possibly mean other than chemistry? I am not arguing that chemistry is not aimed at truth, but “life” — whatever you mean by that — is. That would never be my choice of words.
    I would say: as opposed to chemistry, a free rational agent can be aimed at reason and truth.

  145. 145
    asauber says:

    And carbon is not aimed at being a diamond

    Allan Keith,

    This is a philosophical position.

    The question is why does carbon have properties such that it can be organized into diamond?

    Is your answer “it just does” and your mind closes after that?

    Andrew

  146. 146
    JVL says:

    jdk

    I just read the narrative of Eric’s “model of evolution, which I quote below. I can’t begin to see how this is a realistic model of evolution.

    If your summary is correct then I agree. That model is not even wrong.

    Origenes, gpuccio, Upright Biped: you agree I hope.

  147. 147
    jdk says:

    My post was a complete quote of the short narrative accompanying his code.

  148. 148
    JVL says:

    jdk

    My post was a complete quote of the short narrative accompanying his code.

    Then it’s not even wrong.

  149. 149
    Origenes says:

    jdk & JVL

    jdk: I can’t begin to see how this is a realistic model of evolution.

    Don’t be shy jdk, tell us what is missing. In fact, I would prefer you to offer arguments in support of your claims.
    The same goes for JVL

    JVL: That model is not even wrong.

    Don’t be shy JVL, tell us what the model lacks. Or do you want me to guess?

  150. 150
    JVL says:

    Origenes

    Don’t be shy JVL, tell us what the model lacks. Or do you want me to guess?

    Are you serious? We may disagree on many things but surely we do both agree that his model is hideously flawed.

    Each organism is represented by a bitstring of
    # length L. L is the organism’s complexity.

    How is complexity measured? Some ferns have a genome many times the size of humans.

    Each generation, the organism will create two
    # offspring with lengths of L-1 and L+1.

    Name me one organism that fits this model. And, again, how do you measure complexity? Are you saying if I have two children then one will be more complex and the other will be less complex?

    Each bit in the organism’s bitstring has
    # probability p of becoming corrupt each
    # generation.

    What does this bitstream represent, exactly? Without specifying that how do you know they each have equal probability of ‘becoming corrupt’? What does corrupt mean?

    Consequently, an organism has a
    # probability of 1-(1-p)**L of becoming corrupt
    # each generation

    Is that 1 – ((1 – p)**L) or ((1 – (1-p)**L)? order of operations suggest the first which gives you p**L, why not just say that?

    A corrupt organism cannot
    # reproduce and is eliminated from the population.

    What does ‘corrupt’ mean?

    If L is big then p**L will be very small. Than implies that bigger ‘complexity’ has LESS change of becoming corrupt.

    Take out your calculators and check. A probability is going to be less than one. Any number less than one raised to a power becomes smaller. The higher the power the smaller the result.

    Is that really what you want?

    It’s rubbish.

  151. 151
    Allan Keith says:

    Andrew,

    The question is why does carbon have properties such that it can be organized into diamond?

    Is your answer “it just does” and your mind closes after that?

    No. Chemists and physicists have put in thousands of hours of research into figuring out things like this. Which sure beats ‘it was designed’ and your minds close after that.

  152. 152
    JVL says:

    Right, I made some mathematical mistakes but the system stopped me from editing them in the time limit.

    IF it’s 1 – ((1-p)**L) then that will approach 1 as L increases. But that means you are less and less likely to get something as complex as a human.

    Anyway, there is no indication of how complexity is measured or how it is represented as a bit string.

  153. 153
    JVL says:

    Origenes

    Are you seriously supporting this model? Really?

  154. 154
    JVL says:

    Perhaps Origenes is busy. I will wait for his/her reply.

    But, thinking it over again . . .

    I have no clue how complexity is measured or how it is being represented as bit string of length L.

    I have no idea of how one can use in a model the assumption that each organism will create two offspring, one of slightly more complexity and one of slightly less. Are we not modelling sexual reproduction then?

    Actually, in the end, that part of the model may not matter anyway, it doesn’t seem to be used.

    Continuing . . .

    If the probability of corruption was meant to be 1 – ((1-p)**L) then that probability approaches 1 as L gets bigger.

    If the probability of corruption was meant to be (1 – (1-p))**L then that probability approaches 0 as L increases.

    Either way it doesn’t really make sense. Why should ‘complexity’ determine fitness?

    What does corruption mean exactly? How does corruption affect fitness?

    It’s just all too simplistic and not thought out. In my opinion.

  155. 155
    JVL says:

    I can see gpuccio is writing to the blog on other posts so I guess ‘he’s’ choosing not to respond here. Yet, anyway.

  156. 156
    Eric Anderson says:

    ET @139:

    It takes information to make the atoms. The universe wouldn’t exist without information.

    Yes, I’m aware of arguments to that effect. However, even if we grant such an argument and agree that there was some information required to make atoms, it doesn’t mean the atoms contain information in and of themselves or that atoms are made up of information or any similar claims. That is a very poor use of terminology and just confuses things.

    As an aside, I would also note that it plays right into the hands of people who argue that there nothing special about DNA, after all, there is information in everything — an absurd argument that I have unfortunately encountered from materialists more than once.

    It is quite clear that what we have in the case of DNA is very different than what we have in the case of a rock floating through space, or atoms, or any other physical object in and of itself. The question on the table is: What do we make of this fact?

    We must distinguish between (i) information required to make a physical object, (ii) the physical object itself, and (iii) information that may be represented by a particular physical object.

    Otherwise we are conflating concepts, confusing ourselves, and muddying the discussion.

  157. 157
    Eric Anderson says:

    Bob O’h @126:

    There is no information in the cell . . .

    Others are handling this so I won’t spend a lot of time on it, other than to say in passing that I truly hope you aren’t this misguided. It may be a cute, if annoying, debating distraction to deny the existence of information in biology. But if you really believe this, then you need to go back to square one and start over.

    There are companies that have been founded, university programs that have been established, an entire discipline that has arisen, specifically to retrieve, study and analyze the information in DNA.

    It would be hard to imagine a more blatant example of denial than to claim it doesn’t exist.

  158. 158
    JVL says:

    Sorry folks, it’s 11:30pm where I live so I’ll respond to any messages in the morning. Cheers.

  159. 159
    Eric Anderson says:

    JVL, Iceland? 🙂

  160. 160
    jdk says:

    And here’s Eric’s code.

    # This idea was originated by Salvador Cordova.
    from random import random

    # Initialize the population with
    # a single organism of length 1.
    L = 1
    pop = [L]

    # This is the probability a bit will
    # flip and corrupt the organism.
    p = 0.01

    # Evolve the population.
    while len(pop) > 0:
    # Print the largest organism in the population.
    print(max(pop))

    # Initialize the new population.
    old_pop = pop[:]
    pop = []

    # Create the next population.
    for L in old_pop:
    # If the onganism does not become corrupted,
    # it stays in the gene pool and creates
    # a shorter and longer offspring.
    # Otherwise, the organism is removed.
    if random() > 1-(1-p)**L:
    pop += [L]
    if L > 1: pop += [L-1]
    pop += [L+1]

    # Cull the population to 1 of each length
    # so the simulation doesn’t crash.
    pop = list(set(pop))

    Now, I have done some programming, and am interested in simulations, especially those which iterate from generation to generation, although I don’t know Python, so I can’t follow every step exactly.

    But, in addition to the obvious questions jvl asked (why is length a measure of complexity, what in the world is one child with L+1 and one with L-1 supposed to model, and why is corruption and instant death tied to one “bit flipping”), I’ll also note that the “corruption probability” is set to 0.01. What does this represent?

    I set p =0.0001, and the size of the organism with the longest length (which doesn’t represent anything I can think of, but appears to be the number which the program claims shows that evolution is working or not) appears to get bigger and bigger, showing, presumably, that evolution works?

    This really all make very little sense.

    I will point out, for those that might find this interesting, that the idea for the program originated with Salvador Cordova.

  161. 161
    ET says:

    Allan Keith:

    And carbon is not aimed at being a diamond, and water is not aimed at being a snowflake, yet they are both produced by purely physical/chemical means.

    Yes, in a designed world. And neither exhibit CSI

    The vast bulk of life today and over the last 3+ billion years has no reasoning capabilities.

    Question-begging and irrelevant. There is a reason for it

  162. 162
    ET says:

    Eric Anderson- Everything contains the information it took to make it, at a minimum. Reverse engineering is all about teasing out that information.

    That said it doesn’t mean it is CSI. Crystals are specified but they are not complex. Random stuff may be complex but it is not specified. Nature hits on both of those but not the CSI. Read No Free Lunch again.

  163. 163
    ET says:

    Allan Keith:

    Which sure beats ‘it was designed’ and your minds close after that.

    Good, we don’t advocate that. We say that saying it was designed is just the start. Now we study it as such and find the software that runs the chemistry.

  164. 164
    Eric Anderson says:

    ET, in terms of information, what is the difference between what we see in DNA and what we see in a rock?

    Here is an exercise for you: Take a very simple object, say a smooth cube. Tell me (i) what information is contained in the cube, and (ii) how you located that information.

  165. 165
    gpuccio says:

    JVL:

    “I can see gpuccio is writing to the blog on other posts so I guess ‘he’s’ choosing not to respond here. Yet, anyway.”

    Respond to what?

  166. 166
    gpuccio says:

    JVL:

    Do you mean respond to this?

    “If your summary is correct then I agree. That model is not even wrong.

    Origenes, gpuccio, Upright Biped: you agree I hope.”

    OK, I don’t think I understand well what this “simulation” is meant to simulate, but for what I understand, as it is reported at #160, I would agree with jdk that it does not seem any realistic simulation of any model of evolution.

    But I would say the same thing of all computer simulations of evolution of which I am aware, because no computer simulation I am aware of even tries to simulate NS: they are all examples of Intelligent selection, and therefore mean nothing.

  167. 167
    JVL says:

    gpuccio

    OK, I don’t think I understand well what this “simulation” is meant to simulate, but for what I understand, as it is reported at #160, I would agree with jdk that it does not seem any realistic simulation of any model of evolution.

    A very fair comment. And you say something I should have said: what exactly is the simulation trying to simulate. Because . . .

    But I would say the same thing of all computer simulations of evolution of which I am aware, because no computer simulation I am aware of even tries to simulate NS: they are all examples of Intelligent selection, and therefore mean nothing.

    As an even more general rule: most models are only trying to get at part of the story. One exception (I believe) are weather models wherein the designers are doing their best to simulate the whole enchilada. Which is why they need massive computers processors.

    Anyway, I think it would be best to hear from the ‘designer’ of the code to find out what exactly they were trying to model before making any other assumptions or comments.

    Fair enough?

  168. 168
    JVL says:

    Eric Anderson

    JVL, Iceland? ????

    Nope, the UK.

  169. 169
    gpuccio says:

    JVL:

    “Anyway, I think it would be best to hear from the ‘designer’ of the code to find out what exactly they were trying to model before making any other assumptions or comments.

    Fair enough?”

    Absolutely! 🙂

  170. 170
    asauber says:

    Chemists and physicists have put in thousands of hours of research into figuring out things like this.

    Allan Keith,

    Have they figured it out yet?

    You are just exposing one of the many Scientismic a/mat inconsistencies.

    You say scientists are trying to figure out why there is design in nature (you too, are a designer) while simultaneously denying design exists.

    You poor waifs have a giant crapping elephant in the room.

    You know there is design in nature, but since you don’t know the designer, you suddenly can’t see the design.

    This is not a scientific position, You Who Doth Scream About Science.

    Oh well.

    Andrew

  171. 171
    ET says:

    Eric Anderson:

    ET, in terms of information, what is the difference between what we see in DNA and what we see in a rock?

    It depends. What DNA are you talking about? DNA that doesn’t code for anything is pretty much the same information as a rock. DNA that codes for a functional protein has that- functional information, maybe even CSI, whereas the rock only has the information of its formation.

    Take a very simple object, say a smooth cube. Tell me (i) what information is contained in the cube, and (ii) how you located that information.

    (i) The information that went into making it. (ii) By understanding how things work.

  172. 172
    Bob O'H says:

    Eugene S @ 130, Upright Biped @ 141,
    Eric Anderson @ 157 – I’m not sure any of you are getting my point. Eric writes that “there is information in biology”, and he’s right. But biology is a scientific study. My point is that information is a concept we (humans) use in trying to understand the world, it’s not intrinsically part of the world outside of our theorising about it.

  173. 173
    jdk says:

    I agree with Bob. To quote Seversky again,

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism or a piece of rock. In my view, it is a property of the modeling languages and simulations we use to describe and explain what we observe but to attribute it to what is being observed is to confuse the map with the territory, the model with what is being modeled. It is misleading.

    And to quote myself, :-), from 52

    This is an interesting point. I think it distinguishes those that believe that the world is what it is and our knowledge about it is an abstract overlay on top of it from those that believe that concepts have an independent, and at times primary precedence over physical reality. (That’s a messy sentence, but I have no time for thinking very much about any of this today.)

    The Platonic / non-Platonic dichotomy is, I think, the fundamental philosophical divide between the various viewpoints that get expressed here at UD.

  174. 174
    LocalMinimum says:

    ET @ 171:

    (i) The information that went into making it.

    Interesting. I would venture, though, that it would be some portion thereof, with the remainder being found in what would be called “waste”, if it were an industrial process?

  175. 175
    Eric Anderson says:

    ET, you keep claiming there is information in everything, but you aren’t thinking through whether there really is. This is getting a bit tedious, but if we want to really understand the distinctions, we need to press on a bit.

    One of the things we know about information is that, at a minimum, it can be (a) encoded in a language or other symbolic system, (b) transmitted, (c) translated.

    Tell me, what do you think is encoded in an ordinary rock? What language or symbolic system is it encoded in? What information contained in that rock can you transmit? Can you please translate the information contained in the rock into another language?

    Of course not. The request doesn’t even make sense, because we are not dealing with information. It isn’t there.

    Look, there are only three possibilities:

    1. Physical objects don’t contain information by their mere existence. Yes, they can be made to represent information if they are arranges with specificity, in other words, if they are used as a medium to store information that has been encoded in a symbolic system. But simply by existing (the rock floating through space we’ve been talking about), it doesn’t contain information.

    2. Everything contains information. But the kind of information contained in DNA (yes, of course coding or or similar functional stretches, that is what we are talking about on this thread) is different from the “information” contained in all things. When we’re looking for information in the sense of design detection we are looking for the kind of information contained in DNA. In which case the other kind of “information” is irrelevant to the discussion and we are only confusing things by bringing it up.

    3. Everything contains information. There is no difference between DNA and a rock floating in space. Nothing special about what we see in biology. Move along folks.

    I suppose there is actually a 4th possibility:

    4. Deny that information is real or is in anything. It is just an artificial construct and has no real tie to the real world. Nothing to special about what we see in biology. Stick our heads in the sand and move along folks.

    —–

    Now I take it you would disagree with #3 and #4. Both of these are absurd (Seversky and Bob O’H), I’m talking to you, among others).

    #1 is the right way to view things. See the following and subsequent related posts:
    https://uncommondescent.com/informatics/intelligent-design-basics-information/

    This should clear up your misunderstanding of where the information comes from that you think is contained in the rock. Hint: It isn’t contained in the rock. Like all information, it arises from mental activity — in this case, the mental activity of the investigator. Second hint: You need to start distinguishing between information about a physical object and information contained in or represented by a physical object. These are very different, and the conflation of the two produces no small amount of confusion.

    Finally, if you still insist on #2, then let’s at least be clear that the reference to some vague concept of information existing in all things isn’t relevant or helpful for purposes of identifying whether there is information in, say, biology, that needs to be accounted for. As Seversky noted, a general claim of information everywhere in everything just muddies the water and confuses the discussion.

  176. 176
    Eric Anderson says:

    Seversky, Bob, jdk:

    You guys are staking out an incredibly absurd and irrational position that has very little support in the broader research communities in biology, computing, and bioinformatics. You are also demonstrating that you don’t understand the basics of information — what it is, how it arises, how it gets stored, how it can be discovered.

    Very strange to take such a position so contrary to the evidence, just to avoid having to deal with the key questions head on.

    Just as one example, I happened to be watching a talk yesterday by Dario Gil, VP of Science and Solutions at IBM, working on cutting edge efforts on quantum computing. His take:

    “If you look at an old [computer] punch card and DNA, we’ve come to appreciate that both carry something in common. They carry information.”

    —–

    And yet, all the obfuscation and denial and attempts to redefine information still don’t answer the key fascinating and fundamental questions about what we find in biology.

  177. 177

    I’m not sure any of you are getting my point.

    Your point is not hard to get Bob, it’s just patently wrong. If a rabbit looks up to see a hawk circling above, it does not have a circling hawk traveling through its optical nerves to its visual cortex – it has a representation of a hawk (i.e. information) instantiated in a pattern of neural impulse; transcribed from the environment by the specialized organization of its eyes, to be interpreted by constraints that are in place in its brain which will translate that pattern into a life-saving dash to the nearest burrow.

    This has nothing to do with humanity. The anthropocentric mistake is to suggest that — since we humans can conceive of how it works — we have somehow imputed it into the world around us. No, we haven’t.

    Now, if you want to argue that it’s an anthropocentric mistake to suggest there is “information in everything“, then you have my backing. I’ve been saying it for years. But its simply dull to suggest that information is merely a human construct. Biology has been producing and interpreting information for eons before we ever appeared on the scene.

  178. 178
    ET says:

    1. Physical objects don’t contain information by their mere existence.

    Yes, they do. And I have already covered 2 and 3.

    Tell me, what do you think is encoded in an ordinary rock?

    I have already said- the information as to its formation.

    Read Dembski and Gitt

  179. 179
    ET says:

    I don’t accept the notion that information, as commonly understood, is a property of the genome or an organism

    Science disagrees with and has refuted that claim.

  180. 180
    Bob O'H says:

    Eric Anderson @ 176 – if I’m wrong, you should be able to explain why I’m wrong, not just state it.

    Upright Biped @ 177 – Yes, a rabbit has a representation of a hawk, not the hawk. So the information isn’t “in” the hawk, it’s created (from the sensory inputs) by the rabbit. But the rabbit doesn’t start calculating \sum_i p_i log p_i: that’s something we humans do as a sophisticated way of representing other types of input.

  181. 181
    ET says:

    Bob, Francis Crick explained why you are wrong. Also proof-reading, error-correction, editing and splicing are not reducible to chemistry. as those require knowledge, ie information, to carry out. “It just happens” is not an answer.

  182. 182
    Bob O'H says:

    ET @ 181 – But proof-reading, error-correction, editing and splicing are reducible to chemistry. We know because biochemists have actually shown this.

  183. 183
    ET says:

    What? Then why don’t the synthesized chemicals that mimic exactly those found in living organisms, do these things?

    Please reference the paper or papers that support your claim.

  184. 184
  185. 185
    ET says:

    Bob, You are obviously confused. Just because we can describe something does not mean it is reducible to chemistry.

    Then why don’t the synthesized chemicals that mimic exactly those found in living organisms, do these things?

  186. 186
    EugeneS says:

    Bob

    Frankly, before your post 180, I was inclined to give your line of reasoning more credit than it really deserves. #180 is an unfair one to me. Do you really suggest UB, myself or anyone else who talks about semiosis as an objective phenomenon which biosystems exhibit and which science can help identify, thinks that a rabbit has a concept of Shannon information? I mean, really?! I am disappointed…

  187. 187
    Bob O'H says:

    EugeneS – hm, you’re still not dealing with the issue – you’ve not even attempted to refute my suggestion that information is a human concept that we use to understand the world.

  188. 188
    ET says:

    Bob:

    you’ve not even attempted to refute my suggestion that information is a human concept that we use to understand the world.

    Information would still exist even if we didn’t. Without information there wouldn’t be any organisms.

    But yes “information” is a human word we invented. Everything the word describes is real and not abstract.

  189. 189

    UB: If a rabbit looks up to see a hawk circling above, it does not have a circling hawk traveling through its optical nerves to its visual cortex – it has a representation of a hawk (i.e. information) instantiated in a pattern of neural impulse; transcribed from the environment by the specialized organization of its eyes, to be interpreted by constraints that are in place in its brain which will translate that pattern into a life-saving dash to the nearest burrow.

    Bob’O: Yes, a rabbit has a representation of a hawk, not the hawk. So the information isn’t “in” the hawk, it’s created (from the sensory inputs) by the rabbit.

    Exactly, it is created by the specialized organization of the rabbit’s eyes, and therefore it exists regardless of human conceptions. Information exist as a representation of the hawk, and when it reaches the cortex and brain of the rabbit, it will excite additional information, such as “increase your breathing” and “pump your feet at a time like this”.

    But the rabbit doesn’t start calculating sum_i p_i log p_i: that’s something we humans do as a sophisticated way of representing other types of input.

    Irrelevant. What humans attempt to do in order to measure information doesn’t change the fact that it exists in reality. Rabbits don’t ponder electromagnetic force either, shall we say that it doesn’t exist either?

  190. 190
    ET says:

    you’ve not even attempted to refute my suggestion that information is a human concept that we use to understand the world.

    “That which can be asserted without evidence, can be dismissed without evidence.” C Hitchens

  191. 191
    Eric Anderson says:

    ET:

    And I have already covered 2 and 3.

    By covered, I presume you mean you follow #2 and reject #3?

    So in the case of #2, let’s acknowledge that Seversy’s complaint was a fair point: talking about “information in everything” just confuses the conversation and detracts from the very point ID is trying to make about information in something like DNA: namely, that it is fundamentally different from whatever imagined information we may think is in a rock.

    It is incredibly unhelpful to the entire discussion to conflate the two. I’m not sure why this is hard to acknowledge.

    I have already said- the information as to its formation.

    Read Dembski and Gitt

    Please. It’s pretty rich of you to suggest this. I’m quite familiar with Bill’s work and with Gitt, and could even give Gitt a h/t for getting me thinking through the very point I’ve been addressing.

    What is less clear is why you seem uninterested in learning more about the topic by deeply thinking through some of the key questions I’ve posed, and instead just keep restating the claim that information is in everything. There is a key nuance that is being missed. And will continue to be missed until you are willing to think through the questions I’ve posed.

    I think we agree on much, and I apologize if my tone above seems exasperated. But I think we are largely in agreement on much, so I sincerely hope you will give me the courtesy, not necessarily on this thread, but perhaps in the coming days and weeks on your own time, to carefully think through what I’ve been sharing.

  192. 192
    Eric Anderson says:

    ET @188:

    Information would still exist even if we didn’t. Without information there wouldn’t be any organisms.

    But yes “information” is a human word we invented. Everything the word describes is real and not abstract.

    Well said.

  193. 193
    ET says:

    Eric Anderson:

    It is incredibly unhelpful to the entire discussion to conflate the two. I’m not sure why this is hard to acknowledge.

    I thought I had made it clear there is a difference. That is what CSI is all about- to differentiate between the information in a crystal (not CSI) and genomes (full of CSI) – for example.

    In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. Dr Orgel

  194. 194
    Bob O'H says:

    UB @ 189 –

    Exactly, it is created by the specialized organization of the rabbit’s eyes, and therefore it exists regardless of human conceptions. Information exist as a representation of the hawk,

    No, the representation of the hawk is created by the rabbit, with no reference to “information”. But we (humans) call that “information”. We interpret that representation as information.

  195. 195

    Bob #194

    eh … so it exists, right?

    Right.

    – – – – – – – – –

    (pssst Bob, you’ve now put yourself in the position of arguing that “representations” actually exist in nature, but not “information”, because “information” is just a human concept that doesan’t actually exists, whereas “representation” is not just a human concept, but something that actually exists. In other words, you should probably just stop arguing this point altogether.)

  196. 196
    ET says:

    LoL1 @ Bob- True, Bob, rabbits do not know the word “information”. But they still use it to live or die. They are still made up of it.

  197. 197
    EugeneS says:

    Bob

    “hm, you’re still not dealing with the issue”

    There is no issue, Bob. It is a lack of understanding or (after your post 180) a desire to engage in word games on your part, I’m afraid.

    Like I said, science is out there in order to describe, in its own language, of course – objective phenomena. There would be absolutely no point in it otherwise.

    Semiosis is an objective phenomenon, whether we like it or not. Before Claud Shannon came up with his theory of communication, DNA in living systems contained a message, a series of instructions for the massively parallel ribosomal processor how to synthesize specific proteins. It would contain a message even if we, humans, were unaware of it.

  198. 198
    Bob O'H says:

    UB @ 195 –

    (pssst Bob, you’ve now put yourself in the position of arguing that “representations” actually exist in nature, but not “information”, because “information” is just a human concept that doesan’t actually exists, whereas “representation” is not just a human concept, but something that actually exists. In other words, you should probably just stop arguing this point altogether.)

    I have never said that human concepts don’t actually exist: both the representation and information exist in the sense that they are states of mind.

    If it helps, think about Magritte’s famous painting that isn’t a pipe.

  199. 199
    Bob O'H says:

    Eugene @ 197 –

    Like I said, science is out there in order to describe, in its own language, of course – objective phenomena.

    Hopefully, then, we agree: “information” is part of that language, which is all my point has been, and that one shouldn’t mistake a map for the landscape.

  200. 200
    EugeneS says:

    Sorry Bob,

    “which is all my point has been,”

    No. You are changing the subject from “it’s all chemistry” to discussing stuff irrelevant here such as scientific definitions.

    The real point is your unwillingness to accept the objectivity of semiosis.

    A map is of course not the landscape. However, denying that the landscape exists will not get you anywhere even with the best map possible.

  201. 201
    ET says:

    Information is not a state of mind.

  202. 202
    asauber says:

    Bob is clinging to his religion.

    Andrew

  203. 203

    good grief

    Damn the torpedoes Bob, no matter how utterly stupid it is

  204. 204
    gpuccio says:

    Bob O’H:

    “Hopefully, then, we agree: “information” is part of that language, which is all my point has been, and that one shouldn’t mistake a map for the landscape.”

    A map is never the landscape.

    And all that we know, all our science, our philosophy and every rational cognition are just maps. All of them.

    So, why this special emphasis for information as a map? All science is a map.

  205. 205
    Bob O'H says:

    EugeneS @ 200 – You accuse me of changing the subject, and then accuse me of not accepting the objectivity of semiosis, when I had never even mentioned it!

  206. 206
    gpuccio says:

    ET (and Bob O’H):

    “Information is not a state of mind.”

    Of course.

    In particular, functional information is any specific configuration which allows to implement a function by the object where the configuration is found.

    That seems a rather objective thing: given an object with some configuration, you either can implement the defined function or not.

    What has that to do with “states of mind”?

  207. 207
    EugeneS says:

    Bob

    You started off saying everything in biology reduces to chemistry, right?

    In an attempt to show you this is not the case, I mentioned chess because this simple example illustrates the essence of what is going on in living systems.

    People here, including myself, pointed you to the evidence of semiosis as an objective phenomenon. As an example of it, I pointed you to the objectively existing message processing in organisms.

    In response, you claimed that information was just a human idea.

    Your position is untenable.

    Anyhow, I hope you can see it’s nothing personal 🙂

  208. 208
    Bob O'H says:

    You started off saying everything in biology reduces to chemistry, right?

    Yes.


    People here, including myself, pointed you to the evidence

    of semiosis as an objective phenomenon. As an example of it, I pointed you to the objectively existing message processing in organisms.

    Right, and that reduces down to chemistry, doesn’t it? We know how the sequence of bases in DNA codes for proteins, and it’s all biochemistry.

    So, what was your point about semiosis?

  209. 209
    ET says:

    Bob:

    Right, and that reduces down to chemistry, doesn’t it? We know how the sequence of bases in DNA codes for proteins, and it’s all biochemistry.

    Codes are not reducible to chemistry. Codes are arbitrary meaning they are not determined by physics or chemistry.

    That’s the point. Error correction, proof reading, editing, DNA repair, splicing- none of it is reducible to chemistry. If it was then when we synthesized the exact molecules and put them together it would all just happen. Yet it doesn’t.

    So either the scientists are stupid or it isn’t reducible to chemistry

  210. 210
    EugeneS says:

    Bob

    Code by definition does not reduce to chemistry. Semiosis by definition is sign processing. Sign processing assumes there is a non-physical protocol, i.e. code, logical correspondence or a mapping between the sign and its meaning (i.e. the physical effect evoked by the sign in the system). The mapping is compatible with (permitted by) the laws of nature but arbitrary in relation to them.

    Hoffmeyer & Emeche (1991)*:

    “No natural law restricts the possibility-space of a written (or spoken) text”.

    Kull (1999)*:

    “Semiotic interactions do not take place of physical necessity”.

    Howard Pattee (“Irreducible and complementary semiotic forms”):

    Laws are valued because they express the maximum possible regularity of events. Symbols, by contrast, are valued as information carriers, and information capacity is measured by the minimum regularity of events.[…] The most convincing general argument for this irreducible complementarity of dynamical laws and measurement structures comes again from von Neumann (Neumann 1955). He calls the system being measured, S, and the measuring device, M, that must provide the initial conditions for the dynamic laws of S. Since M is also a physical system obeying the same laws as S, we may try a unified description by considering the combined physical system (S+M). But then we will need a new measuring device, M’, to provide the initial conditions for a larger system (S+M). This leads to an infinite regress; but the main point is that even though any measuring device, M, can in principle be described by the universal laws, the fact is that if you choose to do so you will lose the function of M as a measuring device. This demonstrates that laws cannot describe the semantic function of measurement even if they can correctly and completely describe the physics of the measuring device.

    See here for the references.

    Does the meaning of the posts you write here reduce to chemistry?! Think of it yourself…

  211. 211
    Bob O'H says:

    EugeneS – if codes don’t educe to chemistry, how come DNA transcription reduces to chemistry?

    Why does it matter if a code (or cipher) is arbitrary with respect to physics? As long as the evolution of the code is possible within physics, I don’t see why there can’t be some level of arbitrariness.

  212. 212
    ET says:

    Bob:

    if codes don’t educe to chemistry, how come DNA transcription reduces to chemistry?

    Does it? Is transcription the genetic code, Bob? No. Do you know what the genetic code entails, Bob?

    As long as the evolution of the code is possible within physics, I don’t see why there can’t be some level of arbitrariness.

    Question-begging

  213. 213
    gpuccio says:

    Bob O’H:

    “As long as the evolution of the code is possible within physics, I don’t see why there can’t be some level of arbitrariness.”

    A lot of things are “possible” within physics, but never happen.

    To go back to a classical example, a tornado in a junkyard assembling a Boeing 747 is certainly possible within physics.

    So is the evolution of a symbolic code, or the emergence of Shakespeare’s sonnets from the typing of monkeys.

    Is that your argument?

  214. 214
    Origenes says:

    Given materialism, there is no code. I can agree with Bob on that one. There is only the material stuff that appears to function as a code, but in fact it’s all just chemistry. Sure, there is the illusion of ‘function’ and ‘organism’, but these things do not exist. Obviously, the same goes for scientific research, rationality, morality, freedom and consciousness — if materialism is true, then these things do not exist.
    The realm of existence is exhausted by fermions and bosons.

  215. 215
    ET says:

    Origenes- There must be two camps as some say there is a code but it did not require a mind, somehow.

  216. 216
    Bob O'H says:

    GPuccio @ 213 – no, that’s not my argument. That would be a different argument.

    Origenes @ 214 –

    Given materialism, there is no code. I can agree with Bob on that one. There is only the material stuff that appears to function as a code, but in fact it’s all just chemistry.

    We agree up to here.

    Sure, there is the illusion of ‘function’ and ‘organism’, but these things do not exist.

    But I disagree here. “Function” is a human interpretation of what is happening in the natural world, but human interpretations aren’t illusions (well, not always :-)).

  217. 217
    ET says:

    Bob:

    “Function” is a human interpretation of what is happening in the natural world,…

    It is a word that describes something happening in the natural world.

  218. 218
    EugeneS says:

    Bob

    Transcription is different from translation. In eukaryotes, transcription is needed to transport genetic instructions from the nucleus, where DNA molecules are located, to outside so that mRNA can be later translated there.

    Transcription should be considered in context together with everything else that takes place in the cell. E.g. when a program is executed on a computer, parts of physical memory may be copied as prescribed by the program, which copying by itself could be accounted for by physics. However, this copying is meant to be done for a purpose, which can only be seen in the big picture.

    The same situation is in the eukaryotic cell regarding the duality of transcription-translation. Specific products of transcription, mRNAs, may be needed during protein synthesis later. So, the fact that transcription does reduce to chemistry does not explain the problem away, unfortunately.

    Translation is done, by definition, from one language to another. While transcription treats DNA as data, during translation, in contrast, mRNA is interpreted as a program, not as data.

    Arbitrariness is not just there happenstantially. It is absolutely essential because it ensures that there is freedom of purposeful choice between alternative energy-degenerate chemical states (configurations). This freedom is absolutely needed in order to make sure that a nucleotide sequence carries meaning i.e. specifies primary structure of specific proteins. Without arbitrariness, it is not possible to specify one physico-chemical alternative from among many.

    Without arbitrariness of phoneme sequences a human meaningful speech would not be a possibility. The same applies to written text as well.

    Nucleotide sequences are chemically arbitrary as there is very little chemical bias, hardly any at all, towards any one of the four nucleotides during polymerization. Any nucleotide can polymerize any other. And that is a key enabler of the instantiation of meaning into the physicality of nucleotide sequences.

    If all we had was the necessity of a natural regularity (such as the tendency towards states with min total potential energy in the system), there would be no freedom to specify semiotic relationships. These relationships can be specified provided there is a multiplicity of chemically/physically equivalent states (configurations) to actually mean specific things.

    Again, in chess this is clearly seen. Chess is only possible on a horizontally positioned board (assuming the material of the board and pieces is non-magnetic), the necessity of the laws of gravity, friction etc. by itself can only provide an equilibrium condition for semiotic relationships to come into action. Each configuration of pieces on the chessboard has absolutely the same chemical/physical properties. However, in the context of the game (in the context of semiotic relationships established voluntarily) each configuration carries a different meaning. As to what the laws of nature can do outside of equilibrium states, tilt the chessboard enough, and the game is no longer physically possible.

  219. 219
    Eric Anderson says:

    ET @193:

    Thanks for the additional comment. We’re probably close to the point of diminishing returns (so long as my very specific questions remain unanswered), so I’ll just share a couple of final thoughts on this nuance and then will leave you and others to valiantly deal with the monumental blunders by Bob & Company. 🙂

    I thought I had made it clear there is a difference. That is what CSI is all about- to differentiate between the information in a crystal (not CSI) and genomes (full of CSI) – for example.

    Yes, I agree that DNA has CSI and a crystal doesn’t. The point I’m making is one level deeper. It isn’t just that the crystal lacks complexity. It lacks information altogether. It is a physical object that forms from basic chemical interactions. That’s it.

    There are certainly a few things we could quibble with Gitt about, but I agree with you that he generally has some good thoughts on the topic, so allow me share just a couple of his quotes to wrap up:

    “[Information] is not a property of matter, so that purely material processes are fundamentally precluded as sources of information.”

    and

    “It is impossible to set up, store, or transmit information without using a code.”

    Now, two things:

    1. The material process (the kind of thing Gitt is referring to) that creates crystals is well understood. This process cannot produce information, per Gitt. I agree with him. (There certainly isn’t any information produced as a result of the process that produced the crystal. So if we insist that information is in everything, the most we could possibly do is refer to some vague, esoteric kind of “information” that somehow is contained in the fabric of matter and energy itself — a concept that, even if true, is utterly unhelpful to identifying the information we are interested in for purposes of intelligent design. Again, see my detailed post on that point.)

    2. If we are claiming that information is somehow “contained” in a rock or a crystal, then it must be set up somehow and stored there somehow. Per Gitt, and I agree, this is not possible without a code.

    So, I repeat the highly fundamental questions for you to consider later at your convenience:

    What kind of code is present in a rock? What language or symbolic system is the “information” encoded in? What type of system can we use to transmit that information?

    If you carefully read through the nuances of the post I linked to, and once you think through the chain of causation, you will see that the information you think is contained in a rock floating in space, is in fact created about the rock by the intelligent observer, using the observer’s mind and tools of investigation. It arises fundamentally from the observer, from an intelligent agent’s mental activity — just like all information does.

    This is a nuanced but deeply insightful point related to design if we will let it sink in. If we keep the terminology clear and the chain of causation in focus, I’m convinced we will do a much better job of making the case for design without confusing people in the process.

    Best,

  220. 220
    ET says:

    The information comes from the designer of the universe. It permeates the universe. The universe couldn’t exist without it.

    Crystals have specification but not complexity. Their information content is very limited. As I said earlier reverse engineering is our way of teasing out the information contained in objects.

  221. 221
    Origenes says:

    ET: There must be two camps as some say there is a code but it did not require a mind, somehow.

    A strict materialist should deny the existence of anything but fermions and bosons IMO. Most of them, however, see no problem in talking about “code”, “function”, “organisms”, “decisions”, “morality” “freedom” and what not. But, from a materialistic viewpoint, this behavior doesn’t make sense.
    Concerning code, consider e.g. this:

    But there is no such physical stuff.
    Physics has ruled out the existence of clumps of matter of the required sort. There are just fermions and bosons and combinations of them. None of that stuff is just, all by itself, about any other stuff. There is nothing in the whole universe … that just by its nature or composition can do this job of being about some other clump of matter.
    [Rosenberg]

    ‘Being about another clump of matter’ is not a property of matter. If DNA is not about proteins, then there is no code.

  222. 222
    Bob O'H says:

    EugeneS @ 218 – why does the code have to be arbitrary? if all it does is code the order of amino acids, what difference would it make if it was physically possible for a DNA triplet to only code for one amino acid?

  223. 223
    ET says:

    All codes are arbitrary, Bob. It is the very nature of a code.

  224. 224
    LocalMinimum says:

    What can presuming it’s not a code net us? It frees us from expectations of teleology, or that we’ll continue to find function.

    What are we going to do with that which we have yet to discover function/teleology? Continue searching for function/teleology, or reverse engineering, which will be logically framed with an expectation of such (otherwise you’ll be searching like the child who can’t find anything for themselves in the refrigerator).

    Or we can attribute it as nothing more than a “waste product” of evolutionary processes…which nets us what, again?

    Denial of teleology in biology is denial of the biological research methodology that has built every bit of biology we actually put to use.

  225. 225
    LocalMinimum says:

    I overstepped on that conclusion @ 224. Teleological inferences are not necessary in approaching observed function, but in discovering unobserved function. My bad.

  226. 226
    Origenes says:

    Bob @114

    Bob: … we know the biochemistry of E. coli, for example, and as far as I know it’s all to do with chemistry. This includes DNA replication and gene expression.

    We observe chemical processes. However, we also ‘see’ an organism. Seeing a cat it is not a direct observation. We observe body parts acting in harmonious subservience to a whole. From this we deduce that there is one thing. And it is only at this point that we ‘see’ the cat. The cat who controls its body parts.

    There is no bottom-up explanation for subservience of parts. There is no explanation from the level of the parts. These letters that make up these sentences cannot be explained by self-arrangement. Why not? Because the letters, on their own, are not interested in forming these sentences.

  227. 227
    gpuccio says:

    Bob O’H at #222:

    Excuse me:

    a) If an interaction is direct, and the result is the consequence of physical laws, there is no code.

    So, an enzyme catalyzes a reaction because of its specific configuration: there is a lot of specific functional information, but not a symbolic code.

    b) If the interaction is indirect, and it is mediated by an intermediate which recognizes a signal and couples it arbitrarily to an ouctome, an outcome that the signal itself cannot cause, then we have a symbolic process.

    So, in the translation from mRNA to protein, the coupling between codon and aminoacid is made by the 20 aatRNA synthetases. Those proteins are configured so that they recognize, independently, the codon of the correct tRNA, charging it with the correct aminoacid.

    The codon itself cannot cause the charging of the tRNA. The codon is simply recognized by the correct aatRNA sinthetase, and the protein itself is configured so that it couples that codon to the correct aminoacid.

    IOWs, the 20 aatRNA synthetases are the repositosy of the code, and the true key to its translation.

    So, if the code were not arbitary, it would not be a code. It’s very simple, and I don’t understand your difficulties with the concept.

    A symbol is something that represents something else, but has no direct connection with what it represents.

    A codon represents an aminoacid, but in itself it has no power to incorporate that aminoacid into the protein.

    A word represents something, but it is only a symbol. So is the codon.

    The same thing can be represented by different words. So, indeed, the same AA can be represented by different codons, because the code is redundant.

    But there is more. The code itself can be artificially changed in experiments. That has been done, to a limited extent. See here:

    https://www.tandfonline.com/doi/full/10.4161/adna.29408

    This is possible because the code is arbitrary. It is a code, and it is symbolic.

  228. 228
    Bob O'H says:

    So, if the code were not arbitary, it would not be a code.

    As, so it’s nothing more than terminology. So then my guess is that the answer to my second question @222 (“what difference would it make if it was physically possible for a DNA triplet to only code for one amino acid?”) would be that we simply wouldn’t call it a code. Correct?

  229. 229
    gpuccio says:

    Bob O’H:

    I don’t understand your point, if there is one.

    If a virus is the cause of a disease, we call it the cause. If it is not, we say it is not the cause.

    Is that “nothing more than terminology”?

    We define what the word “code” means in our language, and then we try to understand what corresponds to our definition and what does not.

    It’s called cognition. It’s much more than terminology.

  230. 230
    Bob O'H says:

    Gpuccio – what you describe is simply putting labels on things. If that’s the only reason why it matters whether a code is arbitrary, then it is only terminology. The world natural would work the same way whether we made this distinction or not.

  231. 231
    gpuccio says:

    Bob O’H:

    I really don’t follow you.

    We call a protein a protein because it is a protein. It is a macromolecule made of aminoacids.

    We call a dog a dog because it is a dog. It corresponds to the abstract concept o which we attach the word “dog”.

    So we call a code a code because it has the property of being symbolic. That’s what the word “code” means.

    Everything is “putting labels on things”, when we use words and language.

    But labels are important because they correspong to cancepts.

    So, the word code is important because it means that the system uses arbitrary connections, and therefore it is symbolic.

    That property is important, because it has huge consequences.

  232. 232
    Bob O'H says:

    gpuccio – I think we are actually in agreement.

    Don’t worry, I won’t tell anyone. 🙂

  233. 233
    ET says:

    Bob, It isn’t just terminology as the terminology means something. To be a code means it has specific properties

  234. 234
    gpuccio says:

    Bob O’H:

    OK, it will be our secret. 🙂

  235. 235
    Eugene S says:

    GPuccio to Bob O’H

    “I really don’t follow you.”

    Me neither!

    Bob to gpuccio:

    “gpuccio – I think we are actually in agreement”

    I do not think so, I’m afraid. There is a lot more than just terminology here.

    Bob, you still have to somehow explain semiosis, which is an objective phenomenon. Semiotic causality is inherently different from physical causality (as e.g. in 2H2 + 02 -> 2H2O). Semiosis assumes multiplicity of alternative (physically indistinguishable, arbitrary) states.

    The problem gpuccio and I are talking about is that sign processing is never observed to arise without agency. The reason, from physic’s perspective, is quite simple: this kind of causality does not reduce to physics/chemistry because it is inherently about establishing the symbolic boundary conditions on the motion of matter in a semiotic system, which the ‘laws of nature’ cannot do. The laws of nature and boundary conditions are two absolutely different categories (thank-you, sir Isaac Newton, for clarifying that!).

    In semiosis, we have a formalism instantiated into physicality. Ok, I understand that you and those who are like-minded, suggest that this formalism is a direct consequence of physicality. The problem is, you have absolutely no empirical support for such a claim. This kind of causality from physicality to formalism is never ever observed in nature! Formalism never crystallizes ‘on the edge of chaos’ by itself, to borrow a phrase from S. Kauffman.

    What is observed, is:

    1. physical causality (min total potential energy, for basic types of physical interaction); and
    2. the inverse causality from formalism to physical instantiation of it (as in human technology).

    I really do not follow your reasoning. I simply think you have no case, I’m afraid. I think I have already laid out my argument and I really do not know if spending any more time on this would actually be worthwhile.

  236. 236
    Eugene S says:

    Origenes 226

    Spot on! It is a system level, not ‘physicality’ level. Spikes of voltage in a cable do not mean anything by themselves. It is only at the application level that they make sense!

  237. 237
    Origenes says:

    Eugene S: It is a system level, not ‘physicality’ level.

    Well said. Not being at the physicality level is confirmed by the fact that ‘seeing’ the system is not a simple direct observation. In order to ‘see’it, one has to grasp/understand the whole thing. One has to connect the dots, so to speak. Individual letters do not mean anything by themselves — one has to be able to see words and sentences to get the message.

    Eugene S: Spikes of voltage in a cable do not mean anything by themselves. It is only at the application level that they make sense!

    Indeed. Only if it makes sense it can be seen.

    The “argument” from the other side seems to be the label: anthropomorphism.

  238. 238
    EugeneS says:

    Origenes

    The “argument” from the other side seems to be the label: anthropomorphism.

    Ironically, they accuse theists of anthropomorphism 😉 Their anthropomorphism is manifested in the claim that reality in its entirety can be grasped by human mind. While this is true only to an extent, because universe is not everything that exists, intelligibility of the universe does not follow from their world view at all.

  239. 239
    ET says:

    It can waddle like a duck, quack like a duck, fly, paddle and look like a duck but don’t call it a duck cuz that be the human word. After all the duck doesn’t know.

    We have totally anthropomorphized the world- we have different names for everything. We named them. 🙄

    And don’t even get me started on the French…

  240. 240
    DATCG says:

    Bob @126,

    A little late to this discussion but was surprised at Bob’s assertions. Hope Bob sees this and look forward to his response. A partial repost from comment I made on Gpuccio’s Ubiquitin System Functional Complexity and Semiosis post.

    Bob states,

    There is no information in the cell, only DNA with bases in order.

    Leading to reductio ad absurdum, there is no information in Bob’s cells, therefore no Information exist in the brain cells in Bob’s head.

    Conclusion: Bob cannot make a logical conclusion because he has no active information encoded in his brain cells to compare or make statements with. His brain is just a bag of chemicals with no containment of active, accurate, retrievable and functional information.

    ———–

    Yet, facts are scientist have done work on active information storage and retrieval in reprogramming brain cells of long-term memory. There is evidence information exist in brain cells in Bob’s head and all of our brain cells.

    How else would Bob get home? Go to work? Get any place at all in his life without specific, active information in his brain cells? If Bob cannot store specific, active information in his brain cells, how can he communicate with us?

    Bob may not understand how specific information is encoded in his Carbon-based brain cells yet, but it is. None of us may have specific enough details yet.

    But a recent study on Long-Term memory shows “Place-cells” exist in our brains and can be reprogrammed. To reprogram by definition is to modify, rewrite, redirect a pre-existing program.

    “Summary”

    Long-term memory of specific places is stored in the brain in so-called place cells. Neuroscientists have now ‘reprogrammed’ such place cells in free-roaming mice, by sending electrical impulses directly to individual neurons.

    How to Reprogram Memory Cells in the Brain

    How do we know what happened to us yesterday, or last year? How do we recognize places we have been, people we have met? Our sense of past, which is always coupled with recognition of what is currently present, is probably the most important building block of our identity.

    Moreover, from not being late for work because we could not remember where the office was, to knowing who our friends and family are, long-term memory is what keeps us functional in our daily lives.

    It is therefore not surprising that our brain relies on some very stable representations to form long-term emories(sic). One example are memories of places we have seen. To each new place, our brain matches a subset of neurons in the hippocampus (a centrally located brain area crucial to memory formation): place cells.

    The memory of a given environment is thought to be stored as a specific combination of place-cell activity in the hippocampus: the place map.

    Place maps remain stable as long as we are in the same environment, but reorganize their activity patterns in different locations, creating a new place map for each environment.

    Bob’s is wrong. His assertions are based on materialist reductionism that leads to absurd claims if followed to their natural conclusions.

    To review, Bob claims no information exist in carbon-based cells. Therefore, no information exist in his own brain cells, leading to a conclusion, no information exist in Bob’s brain.

    Q: How is Bob comprehending information and communicating with us? If there is no information in his brain?

    He fails to recognize specific, active information is encoded within brain cells for Long-Term memory – scientific research known since at least 2012(MIT). As research shows, location information is encoded in brain cells.

    It just happens that the information encoded in our brain cells is Carbon-based, not silicon based compounds. Wet not dry. But like a silicon-based compound, cell phone hardware storage medium must be a result of tightly controlled, highly regulated, protected and error-corrected systems design.

    Active prescribed information must exist for protein complexes to be built based upon specific functional information. Pre-programmed interfaces must exist for Wet memory storage allocation, correct relational database information to be maintained and retrieved when required. There must be informational mapping to retrieve the correct information at the correct time.

    Or Bob could be forever lost.

    There are known brain disorders for information corruption in brain cells, like Alzheimer’s and other memory disorders.

    Yes, information in cells exist and thankfully Bob uses that information to talk to us today 🙂

  241. 241
    DATCG says:

    Another concept Bob seems to refuse or accept was pointed out by Gpuccio @132 of Functional Information that is in specific order. This is not just a concept, but a condition that must be met for life to work at all.

    Gpuccio @132 states,

    Bits in order in a soruce code are functional information.

    And functional information is not just something that we use to “summarise” things. If there is not the right sequence in our source code, our program cannot work. If there is not the right sequence in our genes, our porteins cannot work.

    Correcto mundo, agree with Gpuccio.

    Functional specificity is crucial. Without specificity, chaos breaks out. If random mutations were allowed to generate profusely in the genome, proteins are not built. Regulatory systems do not regulate, Editors do not edit and Correction Systems do not correct.

    And it’s not just any order. And it’s not just any information. It is Prescribed, Ordered Information.

    This goes back to ability to recognize differences in:

    Three Subsets of Sequence Complexity and their Relevance to Biopolymeric Information

    Abstract

    Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist:

    Random Sequence Complexity(RSC)
    Ordered Sequence Complexity(OSC)
    Functional Sequence Complexity(FSC)

    FSC alone provides algorithmic instruction.

    Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector.

    Randomness in sequence space is defined by a lack of Kolmogorov algorithmic compressibility. A sequence is compressible because it contains redundant order and patterns. Law-like cause-and-effect determinism produces highly compressible order. Such forced ordering precludes both information retention and freedom of selection so critical to algorithmic programming and control.

    Functional Sequence Complexity requires this added programming dimension of uncoerced selection at successive decision nodes in the string.

    Shannon information theory measures the relative degrees of RSC and OSC.


    Shannon information theory cannot measure FSC.

    FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization.

    No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).

    FSC is aperiodic, but organized structure code in a very specific order – so that as Gpuccio stated Proteins can be built – to specific function.

    And it might be said, Functional Sequence Complexity invariably manifest Organizational structure if unrolled in the right environment.

Leave a Reply