Welcome to the DMZ: The Creation-Evolution De-Militarized Zone

Between North and South Korea there’s a “DMZ,” a De-Militarized Zone. A strip of land a couple of miles wide. A buffer between the two sides. A place where people from both sides can go… and not get shot.dmz_myllissa_2

The DMZ has a number of buildings for peace talks between the two sides.

Evolution 2.0 is a De-Militarized Zone for the evolution debate.

The rules of the DMZ are:

1) Put down your weapons.

If we’re going to talk about this, you don’t come with the intention of shooting somebody dead, even if you don’t like them, even if they’re from a different tribe than you. We have to talk.

2) No hiding behind screen names.

Anonymity brings out the absolute worst in people. If you have to sign your name to what you’re saying online or offline, then you’re a lot more likely to say something helpful.

The DMZ is not a haven for anonymous cowards. If you will not sign your name your opinion is worthless. The DMZ is for people who relish the clash of ideas and have the courage to be right or wrong in public.

3) Assume positive intention.

You need to assume that whoever you’re talking to is there for a good reason, even if you don’t like their values or even if you don’t like their position or their platform or the tribe that they belong to, or their metaphysics or their anti-metaphysics or whatever. You assume that they are here because they want to solve this, and there’s a good reason why they believe what they believe, even if you think it’s nutty.

4. Get to the truth, not the sale.

This is a phrase I got from my colleague Ari Galper, who’s a sales trainer. I just want to know the truth. Everybody knows that if you go to a car lot and the person just wants to sell you a car, regardless of whether it’s the right car for you, that you have this icky used car salesman experience. Why? Because the guy is trying to get to the sale, not the truth. You respect a guy who doesn’t sell you a car because he knows it’s not right for you.

That’s what we have to do in this debate. We have to pursue the truth, pursue the truth, and ignore no verifiable fact. I believe that your will to discover the truth has to be greater than your fear of whatever that truth might be.

We need this desperately. Why?

Because it doesn’t exist anywhere else!

You cannot go to university and have a frank, open, civilized debate about Naturalism vs. Design. Not without getting apprehended by the Political Correctness Police. Some universities will fire professors for suggesting that the universe appears to be planned or fine-tuned for life.

The “pro-Darwin” websites and conferences are boiling with rage and vitriol. Zero tolerance for dissent.

The average church won’t touch it with a ten foot pole.

The creationist websites are offended at the very thought of evolution. Some churches and schools will throw you out in a hot second if you admit you’re an “evolutionist.”

The Discovery Institute, the Intelligent Design think tank, routinely equates “evolution = atheism” in their articles, books and blog posts. Even though the two are not at all the same.

The two main camps – ID and the Darwinists – both omit or downplay the significance of evolution’s “Swiss Army Knife” – the cell’s astonishing ability to re-program itself. Systems like transposition and symbiogenesis.

Richard Dawkins’ and Jerry Coyne’s pro-Darwin books say almost nothing about this stuff. Most ID books say just as little little.

The name-calling, back-biting, snark and vitriol are not even the worst part of the problem.

The WORST part of the problem is:

Both sides are completely talking PAST each other!

Love ‘em or hate ‘em, the Intelligent Design guys raise VALID questions. Their books contain large amounts of competent scholarship.

Their questions deserve to be heard. And yes, answered.

Admire ‘em or distrust ‘em, the secular scientists who publish thousands of papers about evolutionary theory are only doing their job. Their job – their livelihood – is to hunt for naturalistic explanations for how things work.

Neither camp is listening to the other.

That needs to change.

Yes, I know. I heard the guy who just said, “There is no debate. Those guys are idiots!!!”

People from BOTH sides say that.

Statements like that are “exhibit A” of bigotry and prejudice. Because any honest objective assessment shows that both sides raise valid questions. Valid questions deserve respect.

If you’re saying the ‘other guys’ are “idiots” – then we do not have room in the DMZ for you. You will have to lay down your weapons first and agree to a peaceful discussion before you can come in.

But if you want a vigorous but peaceful discussion, this is your place.

Are you with me?

Perry Marshall

P.S.: Many come here (often lacking manners) and attempt to post their opinions, commentary etc. while hiding behind screen names. That is not what a DMZ is for, and those people get banned. 

P.P.S.: Sometimes people have to remain anonymous because they are pastors or scientists, and altering their beliefs can cost them their careers. Those people are welcome to lurk here as long as they like. Beyond that, I don’t have a solution… other than to make the unfortunate observation that the most of the scientists I know who could afford to openly disagree with their profession were those who had other sources of income, or obtained research funding unrelated to the subject of contention.

Photo by Flickr/myllissa.

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59 Responses

  1. Valen says:

    I agree, there needs to be a safe zone for discussion! Just a few observations…you seem to put a lot of stock in the single cell microbe’s ability to adapt and change when under stress. (micro-evolution) But does that translate to more complex organisms? Why hasn’t an alcoholic’s liver somewhere somehow, evolved to be able to synthesize alcohol more effectively? Why have so many species become extinct, but no new species evolved? Not to mention the theological implications of an old earth (sin, death, redemption, etc).

    • Full first and last name, please. That’s one of the rules of the DMZ. No anonymity here.

      “No new species evolved” – that is false. We can observe new species literally every day. See http://evo2.org/darwinists-creationists/

      We know that organisms at every level adapt in real time (plasticity) to changing environmental conditions. See


      http://www.evo2.org/royal-society-evolution – note the Sonia Sultan conversation.

      Some people groups literally can metabolize alcohol better than others. I remember a chance conversation with an Irish guy in San Diego who spent years studying alcoholism, explaining why some lineages are MUCH more susceptible to alcoholism because of a very specific adaptation. (I forget the exact details but I’m sure you could confirm this if you want.)

      More complex organisms from simpler ones – study symbiogenesis. Nature is FAR smarter than both creationists and neo-darwinists give her credit for – at the cellular level.

  2. Bart Nielsen says:

    With no snark or vitriol, could you respectfully discuss any of the lectures (available on DVD from Answers in Genesis) from Dr. David Menton?

    I’m asking specifically about Dr. Menton, so you don’t need to rehash your emotional reaction to Ken Ham or AIG. Thanks.

    • I haven’t seen them.

      I will be happy to discuss any statements made by Ken Ham or AIG without snark or vitriol. Personally I do not believe my comments thus far have snark or vitriol. Rather I have pointed out that Mr. Ham is extremely emotionally manipulative, and I have shown repeatedly that there is no credible or workable solution for speed of light within the Young Earth view.

      • Bart Nielsen says:

        Dr. Menton’s videos are readily available from AIG, and are also available online. Take his lecture, “Formed to Fly.” What do you find objectionable in it?

        • Unfortunately I don’t have the time to go find or purchase someone’s video, watch it and generally comment on it. If you have a specific question I will be happy to give a specific answer.

        • Bart,

          Allow me to anticipate what I think your questions probably are.

          I did a Google search and from the brief description of the video, it looks like your questions are about the DISCRETE differences between birds and reptiles, and that the differences are too pronounced to be the results of gradual changes over time.

          This kind of problem is pervasive in biology. What you see in nature in the differences between species is wholesale discrete changes. Not gradual steps. And of course Neo-Darwinists trip all over themselves trying to explain this as coming from accumulated gradual mutations.

          So without watching the video I would predict that the guy has described all these differences more or less accurately and yes these present a real problem for the standard old-school Neo-Darwinian model of gradual mutations, random mutations etc.

          So let’s understand that in order for evolution to work, it requires MAJOR “rotations of the genetic Rubik’s cube” and they have to be highly coordinated.

          And let’s also understand that evolution on any scale requires an ENORMOUS level of highly coordinated engineering. Beyond anything human devices are capable of.

          Let’s also understand that in order to accept this view of evolution, you have to accept such feats of engineering as an intrinsic, built-in capability of living things. “Autopoiesis”

          As a creationist, Bart, it requires you to embrace a view something on the order of believing that God made living things such that they can adapt to this large degree. (And let me remind you that traditional YEC *necessarily* invokes large evolutionary capabilities, since YEC asserts that every species that now exists descended from a group of animals that would fit on the ark. So the fact that YECs rail against evolution really puzzles me.)

          So the question is, are these “rotations of the genetic Rubik’s cube” possible?

          Well I’ll be the first to admit that nobody has seen a reptile evolve into a bird in real time.

          But what do we know?

          -We know that a protozoan can cut its on DNA into 100,000 pieces and MASSIVELY re-arrange its genetic instructions. In a few hours.

          -We know that you can hybridize two species to generate a third, like emmer wheats + goat grass = modern wheat with a doubling of chromosomes – radical transformation in a single generation.

          -We know that amoeba and bacteria can execute a full symbiotic merger in 18 months, such that neither can survive without the other after the merger is complete – including radical re-structuring of the genomes of both.

          -We know that cells can create information and reverse the normal flow of entropy (they exhibit “negentropy”). Information entropy + millions of years = extinction. NEGATIVE entropy over millions of years is probably quite impressive, given what a protozoan can do in six hours.

          -We know that the mathematics of DNA appear to be based on a fractal mathematical matrix – http://evo2.org/mathematics-of-dna/ – and this “genetic Rubik’s cube” of mathematically based re-combinations does seem likely to exist. (Also see http://www.fractogene.com).

          From my engineer’s point of view, it is FAR more impressive for God to make living things such that they have a built-in, mathematically driven adaptation matrix which is capable of transforming a reptile into a bird by making massive wholesale changes to complete structures – than for God to “poof” create these creatures individually.

          From a general zoological point of view, it is extremely useful scientifically to categorize reptiles and birds as actually being related, rather than just “appearing to be related.”

          From an empirical point of view, we know that massive wholesale restructurings are observable scientific facts in biology. But neither creationists nor atheists like to talk about them. This is the biggest untold story in the history of science.

          From a theological point of view, we don’t have any kind of precise definition of “kinds” at all; we don’t even know whether the statement about reproducing “after their kind” is a general principle or an absolute iron law.

          So there is no theological basis for asserting that new species cannot evolve.

          And again because of the Noah’s ark problem, macro evolution on a major scale is MANDATORY to make the conservative YEC interpretation of history possible.

          And finally from a practical point of view:

          YEC consistently and reliably turns smart, curious Christian kids and adults into atheists. Why? With its inability to square its views with empirical data. Sooner or later people figure out the universe is old. Sooner or later people figure out that evolution in real time of new species and traits is a verifiable observable fact. If you taught them while growing up that YEC is reliable science, they will begin to question EVERYTHING ELSE you have ever taught them. The historicity of Jesus, the NT and everything else becomes suspect. Even though the rest of Christian apologetics is generally pretty sound.

          I’ve never heard of any Christian reading Evolution 2.0 and becoming an atheist. I’ve had a lot of atheists read my book and come to this website who came to faith, or came back to faith, or decide there must be some kind of higher purpose in the universe and begin seeking.

          I submit to you, sir, that Evolution 2.0 reconciles science and religion. To a degree that it becomes obvious how absurd dogmatic materialistic atheism actually is.

          I submit to you that if you adopt my approach in talking to non-Christians you’ll get a lot farther than you did before. Science goes from liability to asset in your conversations.

          And to any irreligious person who only cares about the science, I submit to you that this view serves empirical science, medicine and technology FAR better than either the traditional creationist or Neo-Darwinist views of evolution.

          P.S.: I’m not married to the dogma that birds evolved from reptiles. They might have taken some other evolutionary path.

  3. John Lyster says:

    A) This book should be retitled “Intelligent Design 2.0”. The good scientist puts on his lab coat, rolls up his sleeves and gets to work looking for naturalistic explanations, not because he believes that’s all there is but because this is what he can test and because this is what works. He leaves his “philosophical cap” outside the door of his lab. As Steven Weinberg once said, “Scientists in the lab don’t think enough about God to know whether they are an atheist or not” (but what they do outside of the lab is their own business). The good scientist makes three statements, 1) I have a naturalistic mechanism that is the best approximation to explain observed phenomena that I can offer at this time, 2) I now have a better naturalistic explanation than before but we’re still working on it, 3) I DON’T KNOW. The last statement just has to be the very best statement in science. When he doesn’t know, the good scientist doesn’t “offer a reward” for a naturalistic explanation for a purported “life code” while duplicitously claiming to have “proof” of a supernatural inference “in the meantime” (is this some sort of “pending” God? This entire project has the character of an entrepreneurial game rather than a sincere enquiry). Science begins with an inference it does not end there. An inference without a testable mechanism is mere assertion. Call it a belief system or perhaps a philosophical position if you must, doesn’t bother me just as this is of no interest to “the scientist in the lab”. B) Otherwise, I also observed this bold statement in the promotion of this book on this site, “Discover the 70-Year-Old Nobel Prize-winning discovery that rendered old-school Darwinism obsolete.” Wow, Perry Marshall has written a personal advocacy in a commercial document and apparently it claims to contain a report of a falsification of over 150 years of the carefully built up consilience and consensus of the Neo Darwinian Synthesis in one fell swoop. I’m sure that Barbara McClintock would be proud of her apparent new found status. Not getting a little ahead of ourselves here are we? And all without presenting to the peer review. Quite a feat indeed, Mr. Marshall. Methinks the word “hubris’ is not out of place here. C) Speaking of entrepreneurial games, I love that the search for “Abiogenesis” has now bypassed the peer review in favour of this “Committee of Three”. By the time this fool’s errand in the parallel universe concludes I can imagine that the peer review will likely be well on its way to a real scientific consensus if not already. In the meantime, good luck to all those contributing to this survey, data mining and marketing exercise. Pure entrepreneurial genius. Not sure what it’s got to do with real science.

    • Neo-Darwinism IS obsolete. But don’t believe me or my book. Read the papers that came out of the November 2016 Royal Society evolution meeting. Or listen to the recordings or read the transcripts.

      Neo-Darwinism is dead; nearly all of its major assumptions (evolution is gradual, mutations are random; learned traits are not heritable, natural selection is the only driving force) have been proven wrong ad nauseum.

      I’m not sure why you’re offended that someone’s offering a prize for origin of life. Obviously it’s pushing your buttons.

      I’m glad you think it’s genius. The leading geneticist at Harvard, the leading physiologist at Oxford, and the leading atheist philosopher / historian of science also think it’s a worthy project. The director of Arizona State’s Beyond Center thought it worthy of their lecture series.

      Any experiment that can win this prize will have no problem passing peer review. The book “Matter to Life” by Davies, Walker and Ellis makes a robust case that the information problem is central to life. I define it the same way they do.

      • John Lyster says:

        Yes Perry, I won’t believe you or your book. I’ve seen the link on your site to that Royal Society meeting but it’s late in this part of the world now and off to bed, so I’ll have a look tomo. Yes, I’m sure there is some usual scientific pushback to the Neo Darwinian Synthesis, standard refinements as the science rolls towards this possible “Extended Evolutionary Synthesis”, but I doubt that James Shapiro et al would agree with “Neo Darwinism is obsolete, dead”or “nearly all its major assumptions PROVED wrong ad nauseum”. Wow, such grandeur and self importance (that’s not meant as ad hominem). Ironically I have recently been in email contact with a chap involved with the English climate sceptic think tank “Global Warming Policy Foundation” and discussing their claims that the very same Royal Society has brought about the “demise of science” by presenting its position statements on AGW. They claim this represents the politicisation of the Royal Society based on an extremely obscure “Rule” from its early days when the Royal Society was a very different beast to what it is today. Phew. When I read through your web site (but not your book), I found the same overall sense of hyperbole in presentation. Please, please, science is about MEASURE (sorry about the capitalisation there lol). Your “competition” does push my buttons. Kinda like watching some late night tabloid TV game show I suppose, only much more lucrative……well, in theory. I suppose this is the new entrepreneurial way of doing “science”, put out a prize for a whole lot of wannabies to provide your “Committee” and fellow investors with some ideas while, in effect and at the very same time, tell them they have no chance of “winning it”……I mean, you have already “proven” that “God dunnit” haven’t you? Yes yes, pure genius indeed, but for “real science” I’ll stick with the inexorable and measured peer review as it works towards consensus….should it ever get that far on this question. That’s how science progresses. But no, you’ve already decided that said “prize winner” will have “no problem passing the peer review”. A sort of pre emptive strike before the consensus then? What ever, I just find the whole things sounds like a joke. Perhaps I’m just jealous. I’ve read and watched Michael Ruse and I value his observations but “THE leading atheist philosopher/historian of science”? Really? I guess they would all have their own agendas for being involved and I don’t expect much more than public spin on that so I’ll just leave it at that then. Otherwise, perhaps the director of the Arizona State Beyond Ctr might have Lawrence Krauss’ number and get him on board. Now he’s a man who sure knows how to sell a book with a catchy title, “Universe from Nothing”. cheers jl

        • John Lyster says:

          I’m sorry, please excuse me Perry but I really can’t quite get my head around the idea that you have “proof” of the truly most significant concept in existence and no doubt of profound importance to your good self and yet at the very same time you are running some sort of competition to undo this “apparently” momentous and presumably very personal validation. I’m really not trying to be the smart alec here but there just seems to be something that doesn’t quite stack up here. What happens if/when such “disproof” of your “God hypothesis” comes in? Does this affect your faith in any way? I really suggest that this would not. “God” is a supernatural concept and I find all this mooching around for so called “scientific proof” to be a bit of a game actually. Well I suppose that at least you countenance the prospect of falsification of your “God hypothesis”, which is more than one can say about the “Intelligent Design” proposal. They just leave this vague, non defined inference sitting there with no prospect at all of falsification which no doubt suits them just fine, leaving the media and naïve general public to have a field day and the decent and sincere science left to pick up the pieces. Shameful actually. May I even be bold enough to suggest that you are at one level being disingenuous with this comp or perhaps being a little cavalier with your otherwise undoubted sincere beliefs? Well that’s up to you my friend.

          • John,

            Thank you for your questions and for actually reading and paying attention to what I am actually saying.

            What you are seeing is my own evolution of a quest for the truth across 14 years, from 2004 to the present.

            My Evolution 2.0 book tells the whole story, as do various videos, podcasts and interviews.

            This started out as a God of Gaps argument and that’s precisely what it was 10 years ago. A GOG argument that no atheist has been able solve, by the way. A 21st century digital Paley’s Watch argument, if you will. Based code not being an analogy, but code being a fundamental property of biology. We’ve all known this since the 1950s.

            All codes we know the origin of are designed. This infers design in biology. That’s a fact. Nobody has ever shown us how to get a code without designing one.

            This doesn’t prove God.

            The problem may very well be be solvable. I hope it is. If it is solved, it doesn’t disprove God. What happens next is we realize that nature is even more amazing than we had previously believed.

            And it still leaves us the question of where it all came from.

            I also think that if it IS solved, it will not be solved using the theories or methods that are currently in vogue.

            I am at odds with the Intelligent Design guys because, as you point out, they vaguely refer to design in biology and then act as though this solves the problem. Well in their mind it settles the metaphysical problem but it still doesn’t answer the scientific or technological questions. And the way *some* people (but not all) apply ID, ID becomes a science stopper pure and simple because inquiry stops.

            I was dissatisfied with that. Why? Because I’m an engineer. Scientists cannot say “God did it, that settles it, let’s go out for a 3 martini lunch.” Neither can engineers. So ID comes up short.

            I was equally unhappy with the likes of Richard Dawkins saying “life was a happy chemical accident.” That’s as close to scientific larceny as you can get. Oxford should have fired him the day he said that on NPR.

            So I abandoned my God of Gaps argument and founded this prize.

            I do not believe there is any one place where you step across a dotted line and say “OK, THAT is God!! There’s the proof, right there!”

            Echoing Denis Noble, I also don’t believe there is any privileged level of causation in biology. With living things we are not able to say “See here, it starts with the genes and it all builds from there.” We know this to also be false. Biology is systems within systems within systems, with causality going both “up” and “down” within the system. We do not know how it all starts.

            My hunch is that nature is “turtles all the way down” where you never reach the end of the complexity and the layers.

            The closest you can get to logical proof of God, in my opinion, is Godel’s incompleteness theorem. What it says is that if the universe is rational and logical, then there is necessarily an infinite boundless entity outside of space and time which is responsible for it.

            And if there is not such an entity, then the universe cannot be rational and logical but rather exists for entirely illogical reasons. It perhaps popped out of nothing for no reason at all like Lawrence Krauss claims.

            Thus if God exists, science is valid.

            if God does not exist, science is not valid, because the universe is necessarily inconsistent and therefore not compatible with all scientific presuppositions.

            You cannot prove this one way or the other. I can only point out that you can’t have your cake and eat it too. You can have God and science; or you can have an irrational universe. There is no other choice.

            I flesh this out in detail at


            As for Neo-Darwinism, yes, absolutely, James Shapiro, and Denis Noble, Sir Patrick Bateson, Gerd Muller and Eva Jablonka, and a whole bunch of other people will ALL heartily agree that the traditional Neo-Darwinian synthesis is dead on arrival in 2018. As will recent books by Tom Wolfe and A.N. Wilson; and J. Scott Turner and John Hands.

            “all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved. Moreover, they have been disproved in ways that raise the tantalizing prospect of a totally new synthesis.” Noble, D. (2013). “Physiology Is Rocking the Foundations of Evolutionary Biology.” Experimental Physiology, 98(8), 1235–1243.

            Watch Denis Noble’s address to the international congress of physiologists where he explains the above statement in detail:


            Note the most recent special issue of the journal BIOLOGY about Evolution:

            Was the Watchmaker Blind? Or Was She One-Eyed?

            Living Organisms Author Their Read-Write Genomes in Evolution

            The modern synthesis is obsolete. The empirical extended synthesis directly contradicts most of its major axioms. I am not exaggerating in the slightest. This isn’t bombast. It’s just the biggest news story in modern science.

            Don’t believe me. Read the sources. Scour the papers. Watch the videos. Trace the logic. Examine the arguments and come to your own conclusion.

  4. John Lyster says:

    Perry, thanks for taking the time to respond and for not being defensive about my pushback. You thanked me for “actually reading and paying attention to what I am actually saying”. Actually (yes, actually lol) I find your commentaries to be very interesting, but of course it doesn’t mean I agree. Well that’s no big deal. At some level, my main interest is in thinking about how it is that someone with your undoubted intelligence and training thinks the way that you do. Sorry if that sounds patronising but there’s a lot of stuff out there that I wouldn’t waste the time thinking too much about. To be honest, I find this business of the parallel universe of highly trained scientists (think Creation Ministries International https://creation.com/about-us#who_we_are ) being Creationists to be most intriguing. I continually ask myself, “just what the bloody hell is going on here?” (sorry, I’m Australian and we have a more flexible use of the English language, but I promise that was only meant in humour). So perhaps a little “couch psychology” if I may please. I think it’s clear that you are a dynamic and successful person so none of this is meant to be personal (except where I totally disagree with you lol). General comments: I have a different faith background to you and actually I think a lot of this percolates through to our world view and hence interpretations, well nothing rocket science about that of course. I think it’s also clear that we have different personality styles, I would think that I am rather more measured and reserved compared to your, shall we say, exuberance and of course this will mean we simply interpret things differently, such is life (please excuse me but I think the most outrageous example of your exuberance has to be your claim of “proof” of the supernatural from what is essentially an untestable inference. Lashings of ID here. For me this is pure belief system forcing “your science” to give you the answer you are looking for. I do hope that you do not mind my strong challenge here. I just want to be honest with you). I come from an Irish Catholic tradition (in Australia), lapsed, and you have what I presume is the American Protestant tradition but we both share a tertiary training in the sciences, mine is in the life sciences (undergraduate level and none in formal evolution theory), yours in engineering. A good blend. Otherwise, as far as philosophy and socio-politics is concerned, I am pure layman. Putting aside personality differences and entrepreneurial accent, I sense that our different faith traditions and orientations comes through on our interpretations in ways that seem to be irreconcilable, as in “agree to disagree”. In the end this includes our interpretations of this interesting matter of Evolutionary Biology. In a nutshell, Catholicism is from a European tradition and, as such, well integrated with the history of European philosophy and the “evolution” (dare I say it) of Science from that project. Due to its history, the Catholic Church is well versed in matters science, I think this shows up with its present approach to the issue of Climate Change. The American Protestant tradition seems to me to be much more focused on a direct appeal to the Bible and its contents, less philosophically based (??) and certainly not having bounced up so much against science in its history. Hence this gigantic, present day, clash with the science of evolution and which I sense that you (and your brother) now personally struggle. In my Catholic upbringing I barely read the bible at all, it hardly seemed to be on the radar in my schooling. It seemed to be just some background reference manual, perhaps that’s just me or the way it was taught at my schools. I actually wasn’t formally taught evolution at school as I didn’t study biology (funny about that), however there was simply no sense that the science of evolution was an issue to give much thought to as its acceptance appeared to be a given. I’m sure my school’s biology curriculum would have been mainstream, particularly as the Catholic Education system in Australia is extremely large and tax payer supported. In any case, I now understand this to be the Catholic teaching, something that I think comes through from its European tradition. I always associate this “controversy” as something “those evangelicals and Americans get themselves worked up about”. In any case, I would think that something we do both historically share is a faith orientation towards a personal and directly intervening supernatural agency. However, I must say that this looks like where we now walk different paths. You appear to still retain this to a large measure and I think this shows in your writings and on your web site. You must see direct supernatural agency in the natural world and of course the bible is the “source code” for understanding this agency. As far as I am concerned, I feel as if I have followed the infinite regress of the turtles all the way back to a Greek style, philosophical First Cause, that being the explanation of our law bound Universe that is the Natural World. I have read your extremely interesting page on the “Gödel Incompleteness Theorem” and while I understand it to be a dry statement about the limits of mathematical analysis, I appreciate your “theological extrapolation”. In the very same way I think of the Leibnitz Argument from Contingency as being a plausible philosophical assessment of the First Cause of the Natural World. Personally I take these as philosophical statements that are not religious and so from this I presently view this First Cause as simply the inexplicable Absurdity beyond and external to our law bound and intelligible universe. Unlike your good self, I do not consider that such consideration of this “external explanation” comes from the Christian faith tradition, indeed I consider that the European Christian tradition borrowed this concept from the European philosophical project. I consider formal religion to be simply another naturalistic world phenomenon that encompasses the very human desire to “invent god in our own image” as a way to overcome the inherent existential angst of our existence in an intelligible universe that appears to be an emanation from this disquieting absurdity that lurks below the surface. In this way then, I view all attempts to religiously label and characterise this absurd “First Cause” as naturalistic symptoms of our human nature. This includes anthropomorphised concepts of intelligence, design and agency. Of course you have a very different perspective and this appears to percolate through to your strongly held affinity for direct and personal supernatural agency and to what I consider to be your equivocation of human (naturalistic and therefor examinable) intelligence with the philosophically putative supernatural (therefor not scientifically/naturalistically examinable) intelligence. A supernatural intelligence, by definition, does not have or leave an examinable footprint. Otherwise it is no longer “external”, it is simply another prosaic naturalistic being, the proverbial grad student on Andromeda Galaxy and we are his simulation experiment. I can see this come through in all of your writings that I have so far had the pleasure to read. In this way, while we can both “agree to disagree” about philosophical matters such as the place of the external supernatural first cause in this natural universe, my point is how I feel this affects your assessment of science, what it claims and what it can claim. This is the question is it not? I feel that I can see how your sense of direct and personal agency (as revealed by the Bible that is clearly very important to you) affects how you interpret and write about science, a subject that you have undoubted and abundant knowledge of. I’m not here to “correct” your philosophical position on the supernatural, what I call “the absurdity” (because, in all honesty, I can not ascribe to it any of the characteristics that religions do) however I do question how this affects your (and of course the ID people) interpretation of science and so the modern evolutionary synthesis. In this way, I think that Science does have a lot to say about the naturalistic claims of the humanistic phenomenon of religion but it actually has absolutely nothing to say about concepts of the supernatural, call it God or “the absurdity that is the essential first cause and explanation of this contingent, law bound, naturalistic universe”. Naturalistic science, the science that works, can not and will never prove or disprove the philosophically supernatural, by definition. Inference without a testable mechanism is mere assertion of one’s belief system and imposing this on science. I would urge you to please consider that one point and am happy to read your thoughts and any pushback. I always leave a little room for personal doubt and scepticism. As an aside, I have briefly met the great man Richard Dawkins, a man I sense is of immense personal integrity, honesty and what I would label, blistering objectivity. However, as a philosopher of science, I think he makes a great science educator. I am irked by the sense that he is somehow seen as ‘the spokesperson” of science and evolution and I wish that he would speak more of his “philosophical materialism” and let the “methodological materialism” of science be. Otherwise I do like his sense of humour (OK, I’m very dry like that) and I love his politics. If I was an American I’d be “All the way” with the Democrats. At one level, the philosophies of people like Richard Dawkins and his mate Sam Harris are both confronting, even a little depressing if you let it get to you. Yet on another level, it is both challenging and, at the very least, exactly how every scientist should be thinking while “in the lab”. As far as I can tell, these guys are doing a little reprise of Rene Descartes in excoriating all of their “normal human psychological biases” towards the external source code back to the tabula rasa and truly and relentlessly pursuing the possibility of naturalistic explanations for ALL the phenomena we observe WHILE IN THE LAB. Whereas Descartes’ was a rational tabula rasa I think of these chaps as doing an empirical as well as rational version, hence they must not presume any supernatural agency at all while they are doing their work. Not because they are “right” (what ever that is) but because this is “pure science that works” (purported claims of Kuhnsian paradigm shifts aside but I don’t like the ID peoples’ chances of sourcing such a shift as they claim, quite the opposite. If anything, I think that it is the “New-Atheists” who can lead a paradigm shift IN THE LAB……..what they do outside it is up to them. I think a lot of their “Atheistic energies” as being merely a way to psych themselves up to maintain the rage for “good science”. In any case I gather that Sam Harris actually eschews this as a personal label whereas Dawkins has, at one time, canvassed the overt use of this label as more of a political strategy against the excesses of religious claims and of course the attendant socio-political conservative agenda. By this I mean “Atheism” as commonly understood to be “philosophical materialist”, as opposed to “A-theism”, the lack of belief in a personal religious theity and all of its purported naturalistic accoutrements. I’m sure that Harris would happily subscribe to the latter, as would I……for now. Phew, all shades of grey). I think the “New-Atheists” are an example of how every good scientist should think, but what they think “outside the lab” is another matter. If people like Sam Harris eventually manage to obtain a naturalistic explanation of consciousness (surely the last frontier for naturalism) then this may put the naturalistic claims of religion under the pump but surely NOTHING can affect the philosophical end to the infinite regress that “explains” the reason why this universe is naturalistic rather than absurd. Perhaps it is they who are on the proverbial fool’s errand, but while they are “in the lab” then I say “go for it”. Regarding your “competition” (sorry), the cynic in me might suggest that it is purely a marketing exercise for your brand, but I can also see that you are very sincere in your faith/science project. I think it’s always foolish to button hole peoples’ motivations, sometimes I even wonder what motivates me in what I do. I would think that the academics on your team might have in mind a gigantic “peoples’ boot camp”, who knows what may come out of left field and hey, “what have they got to lose?” (if not possibly a little academic prestige). They say that science is on the threshold to a working hypothesis of abiogenesis so all inputs gratefully received I suppose. Will you pay out on the recommendation of your Committee or when one of you heads off to Oslo for the real prize? (OK, that’s my dry humour). Either way, God will not be affected and I’m sure the Catholic Philosophers will watch with keen interest should this project, or the mainstream project, get traction. They will watch on with complete ease I’m sure, what a successful result might mean for some of the more “bible” based versions of Christianity remains to be seen. Continued denialism has a long history in many areas of science. With that “background briefing” in mind, if I may, I will make some more direct observations of some of what you have written and said in “That Video”, but this will be a little ad hoc.

    -Philosophical positions are plausible or implausible. Naturalistic explanations are compelling or not. The only “proofs” are abstracts, such as human made definitions and mathematical proofs, all else is about permanently provisional Bayesian shifts in my understanding.

    -I would describe “Atheism” as the implausible philosophical position that all is existence is purely materialism. I found your discussion regarding Gödel’s theorem provided me with a little Bayesian shift further in this direction……….for now.

    -I would describe “A-theism” as the plausible philosophical position that personal, interventionist religious theities do not exist……for now. I consider such abstracts to be symptomatic of the naturalistic world phenomenon that is religion.

    • John Lyster says:

      -I am no Noam Chomsky on language and I suspect that you have more understanding of Information Theory in your left toenail than I have in my cranium but I do reserve the right to make some observations. Mistakes and deficiencies in my thinking will undoubtedly abound. Such is life and the learning curve. I don’t expect your world to be turned upside down by my “couch science”, but I do hope you can find it to be interesting.

      -patterns vs design/information. You label non life naturalistic phenomena such as tornadoes and snowflakes as having physico-chemically sourced naturalistic patterns whereas the “patterns” of DNA molecules represent this inferred agency’s handy work. As far as I can tell, both phenomena contain molecules, atoms and sub atomic matter/energy and it is our human (naturalistic) intelligence that ascribes these arrangements as either naturalistic patterns or representations of intelligent code. Because I am no expert on such matters I will take it that a) we have a perfectly acceptable naturalistic mechanism that explains the arrangements of the matter seen in tornadoes and snow flakes, b) we don’t have such an acceptable naturalistic explanation to explain the arrangements of the same sort of matter seen in the DNA (hmm, I could contest that but for now, I will accept “We don’t know”). The job of the good scientist “in the lab” is to keep looking for said testable naturalistic mechanism of the arrangements of matter in the DNA while loudly and proudly proclaiming, for now, “I DON’T KNOW”. What any scientist thinks and claims outside the lab is his own business. In the very same way as Richard Dawkins needs to separate his “philosophical materialism” from his “methodological materialism”, may I respectfully propose that you (and the ID people) apply a similar principle.

      -you ascribe an “apparent language” to this putative DNA code. Please allow me to do the very same to the “patterns” of various types of tornadoes. I’m no meteorologist, however I will propose that there are various different types of volcanoes, some tall and thin, others V shaped, others still squat and bulbous. If we were to label these patterns, each with a letter of the (human world) alphabet, and watch as a group of tornadoes came into view then pretty soon we might indicate this scene with letters on a data file in the same way as the lettering ascribed to the molecules and atoms of the DNA. Before long the pattern of the human (natural intelligence) created volcano letters might begin to look like an ordered sequence of letters on our data file and before too long our agency seeking brain might begin to see some sort of hieroglyphic “code” taking place. The natural patterns of the molecules and atoms of the volcanoes are unrecognisable to us in any way that is meaningful, however when we use our natural world human intelligence to label them with letters on a data sheet, suddenly we might just begin to think of them as providing a source code. Now I’m not trying to tell you how to suck eggs on the matter of “codes” and information technology, however a part of me simply regards this idea of labelling patterns of atoms in a long molecule such as DNA with letters as the naturalistic, human intelligence creating its own language which it then re interprets as supernaturally inspired. Personally I would urge that the patterns in the atoms of the DNA molecule have the same quality as those in the tornadoes and snowflakes and that there is either a naturalistic mechanism that we have explained and measured (as appears to be the case for the tornadoes) or that we have not (in the case of the DNA). Personally I would think that we do have a naturalistic explanation for the patterns of the atoms in the DNA but that is not my point here. My point here is that there seems to be something exceedingly circular about ascribing meaning to a bunch of “letters” that our own human intelligence has created and claiming that the meaning has come from a supernatural source. I suspect that there is no difference between the naturalism of the arrangements in the DNA and those in the tornadoes, except the labelling of these patterns in the DNA molecule has created the impression of an intelligent sourced language in a way that was not done with the tornadoes or snowflakes.

      -I question your discussions of “random mutations” and “natural selection” throughout your commentaries, seemingly raising them as separate issues when in fact they are but two different components of the very same two stage process. Numerous references to the so called “randomness” of evolution without any reference to the fact that this is essentially entwined with the other stage “natural selection” which makes the “whole” non random. Then I noticed your rebuttal page on Jerry Coyne’s review of your book that simply referenced “natural selection” as his one stop answer to everything…….the proverbial explanation for everything that explains nothing. Where have we heard of that one before? Well I suppose Jerry has read your comments but I doubt that he is crying in his soup. Perhaps it might have helped if the explanation for Evolution was simply labelled as one process, try “randolection”. I’m not kidding. I would suggest that this be the new word to describe what is after all two components of ONE process. The trouble with the present label is that it is TOO honest and TOO explanatory. What would be better would be to give the entire process an obscure name that indicated its hybridization of two components as the totality is greater than the sum of the parts. It might also hopefully temper the emotional interpretations behind the words “mutation” (always makes things “bad”) and random (Godless and without purpose). I personally view this “dual process” mechanism in the same way as I would any other naturalistic chemical process, it simply works by the laws of nature and has no particular end game. It’s up to our naturalistic intelligence to work out our purpose and actually I feel comfortable that this is entirely compatible with any philosophical supernatural, non anthropomorphic and absurd “intelligence”. Clearly the Catholic Church has no, in principle objection to the naturalistic aspects of this chemical process, however I presume that they consider it is guided to a philosophical purpose and end game. Beats me. Move out of the lab and its what ever philosophical position is most plausible for you, but let’s at least get the lab right.

      -I note your discussion of the google ads random generator and the apparent problems with generating an “intelligible code” within a reasonable time. I feel like I’ve seen this discussion a number of times and while I am just a layman in terms of evolutionary biology I am aware that a major component of the Neo-Darwinian Synthesis is the sophisticated mathematical analysis of “population statistics”, particularly three gentleman JBS Haldane, Sewell Wright and the giant of them all Ronald Fisher. The latter, having lived out his final days in my home town and now buried in our main Anglican Cathedral. Well that’s our small claim to fame (he was an Englishman). I’m quite relaxed that this analysis suitably answers all such examples of “inefficient random generators”, not to mention concerns with punctuated equilibrium and the Cambrian Explosion that so concerns one Stephen Meyer over at the DI. There is a lot in science where one layman such as myself can not hope to be the “universal expert” and so one defaults to the general consensus and expects this to respond to the concerns of people like Meyer. There are many examples of highly qualified scientists who become “arguments for authority” for pet hypotheses when not making much headway within the consensus. Their cries of conspiracy carry no weight with me because I appreciate how science works and that it actually demands challenge and “disproof”. I appreciate this, not because one is a naïve “believer” but because one understands that this is how science works. To believe otherwise is to believe in the conspiracy theories of science denialists. I see great parallels in the creationist (extremist religious) approach to the science of evolutionary biology and the politically inspired objections to climate change (AGW). If you don’t mind, I think that the random generator idea is too simplistic to account for what goes on with real world evolution and I believe that the simplest explanation goes to Richard Dawkins’ idea of “climbing Mt Improbable” (Dawkins the scientist and educator, not Dawkins the philosopher or political advocate). He gives the analogy of picking a bank vault lock. When ever the correct number is picked then this becomes the baseline for picking the next in the combination. You indicated the degree of impossibility of “picking” two correct neighbouring numbers/letters however one doesn’t have to begin from scratch every time one begins a random generation as appeared to me to be indicated by your analysis. If you don’t mind my suggesting and without going into the sort of detail that is beyond my scope I think it’s pretty clear that the sort of statistical analysis provided by the geniuses of population statistics is much more sophisticated than in your example. When watching this video I did think of something else. You indicated that the random generator would necessarily generate lots of meaningless words that would fail before it “hit the jackpot” that you were looking for. As far as I can tell this goes to the issue of interpreting evolution as somehow being directed to some sort of goal focused end game. In your example, YOU (the naturalistic intelligence) chose what worked and what didn’t and in this case, the generator was goal directed to change “Easy to Fast” as its “successful outcome”. Surely this is not what is happening in real world evolution? In the real world, “success” is measured by adaptation to the environment and this means that any number of combinations can be successful. In this way then, the real world generator will create many more “surviving” codes which can all then each provide further individual generator opportunities for the totality to eventually produce the “individual successful end result” that you have prescribed and in good time. In the real world, evolution will end up actually generating multiple generators and in any case “success” is not being measured by the goal centred search for the one particular “golden nugget” combination, success is endless combinations, not any particular one. Not to mention that each “successful combination” becomes the starting point for subsequent generation without having to “begin from scratch” at all times, so to speak. I’m not a statistician but I think that the simple point to be made here is that population statistics is a vastly different ball game to that of your random generator. If you don’t mind, I do feel that your interpretation of this matter is quite possibly clouded by the fact that you appear to consider the evolutionary processes to be somehow “gaol focused” towards some particular combination of “letters in a language” when in fact this is simply not the case. May I be bold and suggest that this comes from your “code centred” analysis of DNA sequencing as opposed to the “phenotype adaption centred” analysis of DNA. Evolution is about what phenotypes best adapt to the environment and this is going to have a completely different impact on the statistics and timing of “successful outcomes” than your “letters and numbers” focused random generator. I feel like I do have just a sense of this and make no claim to expertise however I think that, as per usual, there are statistics, damn statistics and lies and one really needs to be careful of the approach that is used to analyse what is going on here. For a high profile person such as yourself I am sure that it would be worth your while checking with an expert on this area. That is unless you are of the opinion that the population statistics of the Evolutionary synthesis is some sort of closed shop collusion to “prove” some sort of materialist agenda.

      -I note your discussion on the mutation induced irradiated fruit flies being a purported example of how evolutionary mutations will only ever yield in deleterious results and extinctions. It is my understanding that this was an example of “Artificial Selection” being directed to induce these certain changes and bearing no relationship to the undirected (except towards adaptation) “Natural Selection”.

      -you mentioned in your recent email the concept of the so called GOG argument that “no atheist has been able to solve”. In science, one must always provide a positive argument, one can not default to the negative argument of “you don’t know, therefore I must be right”. In the lab, ALL scientists should be methodological atheists and so, in this way, if he has a gap in the knowledge then he simply says “I don’t know, so I will get back to work and keep searching”. GOG arguments are simply a logical fallacy that no good lawyer would fall for. To me, science is in many ways, just like the law. I guess it all gets back to their shared source code (dare I say), Greek logic and philosophy. Actually Richard Dawkins is big on this, I regard him as a champion of how a good scientist should think but what he thinks outside the lab is up to him. As I wrote above, I do wish he would make this more clear. GOG is a negative argument that fails and is really at the core of the failure of the ID project which seeks validation by chipping away at the inevitable gaps in the Evolutionary Synthesis rather than presenting its own positive argument (testable mechanism). The Catholic Evolutionary Biologist from Brown University, Ken Miller, explains this very well in a debate with ID’s Paul Nelson. https://www.youtube.com/watch?v=04XL1Li0dI8 For the sake of this discussion I am not at all interested in the fact that Ken Miller is a Catholic, although it does indicate that religious inspired scientists can be perfectly effective at their job. Apparently he does have some sort of Catholic inspired philosophical position on “Quantum Indeterminism” but he doesn’t present this as a scientific theory.

      -you mention that all codes are designed, THEREFOR ……………..DNA’s source code is so designed. Well this is highly inductive and while I appreciate that you have elsewhere claimed “this is nothing more than normal scientific reasoning” (or words to that effect), I would respectfully assert that the “best answer” (not perfect answer) to the “problem of induction” in science is to provide the testable mechanism to your inference and then proceed to the endless, permanently provisional, cycle of inductive/deductive reasoning that is the hallmark of the scientific method and consensus. One simple inference to an untestable claim is just assertion and is merely the beginning of this cycle, not the end of it. In an imperfect world of uncertainty, “science never ends” is how it “best” tackles the “problem of induction”, it does not stop at the first inference and then “down tools” in self satisfaction. This is how science gets to the point of “compelled to believe that we have the best approximation of the nature of reality” without ever being certain.

      -While I don’t have the background to counter your discussion of DNA as representing the putative “code”, I would also respectfully oppose your assumption that “all codes have a NATURALISTIC design, therefor “we don’t know” allows us to infer a SUPERNATURAL design”. As far as I can tell, this is straight out of the land of ID. Indeed I found myself to be confounded by your continual conflation of NATURALISTIC design/intelligence/code/information/agency with SUPERNATURAL design/intelligence/code/information/agency as if they are one in the same thing. Naturalism carries with it an examinable footprint, supernaturalism is, by definition, capricious. There’s just nothing to test, this is philosophical conjecture, not science. You are perfectly entitled to make a philosophical assertion that DNA has some sort of emergent supernaturally sourced “code”, but you are operating outside of the lab when you do this. Personally I consider that Evolution by “random mutation and natural selection” (both acting together) is a perfectly valid NATURAL explanation for the putative “code” in DNA, but I can see that this will be a dead end to push this point here with you. Examining and measuring the footprint of naturalistic intelligences such as ancient societies is just how anthropologists and palaeontologists work. If they see something with a footprint (the way the stones were cut and arranged, the tools they used) they can infer (and proceed to test) hypotheses about the sort of society they are looking at. They never claim “we observe something, but because we don’t know what phenomenon explains this then we will claim a hypothesis of a PENDING supernatural intelligence until something crops up”, while offering a prize for every tom dick and harry to come up with something. Science must provide positive (testable) arguments or else it says “I don’t know, but we’re still looking”.

      -Conjecture if I may please. I don’t know if you appreciate my point above. I feel that the conflation of natural intelligence (us) with a putative supernatural intelligence (religious God) AS IF they were the very same thing is the “source code” of all the problems with ID (and yes, your good self if you don’t mind my saying so). The very same problem flows through to design and so it seems, information. I bet you are a world expert on that naturalistic phenomenon, Information Technology, but just because we use the same word (intelligence, design, information) surely doesn’t mean we are talking about the same thing from a scientific perspective. I’ve mentioned above why I think this conflation is wrong (natural measurable, testable uniform, footprint vs supernatural untestable capriciousness……by definition). So why does this happen with people? My conjecture is that this is because of the religious inspired/enabled/associated tendency to anthropomorphise the supernatural in a way that seems to “naturalise” it. We ascribe natural world, human qualities to our Gods and before we know it, they become akin to our best mate or worst enemy. At some deep emotional level we seem to be hard wired to do this just as we also ascribe anthropomorphic agency to naturally occurring, non intelligent phenomena such as rustling wind in the savannah or spooky noises in the dark. While this can be argued as some sort of evolved phenomenon that provides us with a survival advantage in the natural world or perhaps it is a legitimate philosophical position to adopt in relation to the supernatural, I don’t think it helps in being a good scientist if it leads us to “naturalise the supernatural” in the lab. For someone like Richard Dawkins and Same Harris (or myself?) I think it becomes very easy to psychologically “hop into the lab mode” and become the necessary methodological materialist. For sincere religious based scientists, I think that this is simply something they need to be aware of and work hard to counter otherwise they are no longer the good scientist. Harder, but not impossible. Perhaps psychologically picturing themselves or even formally putting on the “materialist hat” when they go into the lab as a way to overcome what appears to be this natural human tendency to anthropomorphise the supernatural in the same way as we can anthropomorphise unrecognised natural, non intelligent phenomena. When we don’t know or understand something we seem to anthropomorphise it and we can see this especially in children before their rational minds develop. I won’t be so bold as to “blame” religion for the way that this tendency makes it hard to work successfully in the lab as it could perhaps be argued that it is this natural tendency (to anthropomorphise the supernatural) that causes us to be religious in the first place. Nevertheless I do feel that the religious mindset enables this tendency and can make the required “materialist mindset’ harder to obtain when entering the lab. Well this is all just conjecture, the important point is that the good scientist must adopt the “scientific mindset” when he is in the lab and fight what appears to be this human tendency to “naturalise the supernatural”. Depending on one’s world view, I would contend that such mindset comes easier to some than others, but that doesn’t mean that it is not possible for any scientist (religious or not) to adopt the “non anthropomorphic” mindset in relation to the supernatural. I feel that this is what makes science and scientists work better. Of course the situation with ID is a disaster. Rather than appreciate and counter the natural tendency to anthropomorphise the supernatural (philosophically OK to do in their churches) hey, the very thing that causes them to naturalise the supernatural in the lab, these people want science to flex and bend to their socio-political ideology. For them the project of naturalism is a “materialist plot” and the purpose of science is to somehow examine “all knowledge”, even to the point of making science examine the supernatural. This makes science unworkable. I’m sure you appreciate the last point I’m saying here even if the rest is a little convoluted. In all of this, I make no claim about the putative intelligence of the supernatural, be it anthropomorphic or “absurd”, I simply say that, for the purposes of science, it is a conflation to equate supernatural intelligence with our natural intelligence because we don’t have a measureable naturalistic footprint to examine and test. The nature of any supposed supernatural intelligence is, BY DEFINITION, purely philosophical. I do contend that the religious (inspired, enabled, associated) tendency to anthropomorphise the supernatural makes it harder but not impossible for the religious scientist to adopt the right mindset in the lab. May I suggest that your “random generator” statistical analysis of DNA sequencing suffers because of your belief that it is the golden nugget of the “secret code” itself that is the ordering agency of the DNA rather than the phenotypic adaptation imperative.

      • John Lyster says:

        -some specific observations from your last email……………

        -“A GOG argument that no atheist has been able solve, by the way. A 21st century digital Paley’s Watch argument, if you will.” Wrong burden of proof. Each proponent in a debate must provide their own positive argument, it is not sufficient to claim validation by providing a negative argument against your opponent. I suspect that you are claiming that Evolution does not provide an explanation, an assertion that I disagree with. In any case, if I granted that you are correct on this then this still does not validate your position. Untestable inferences to supernatural agencies are not a valid positive argument for reasons I have explained elsewhere. Where a purported gap has been presented it is perfectly acceptable for the answer to be “I don’t know”, which then becomes the driver of further research for testable natural explanations, notwithstanding that some level of gaps will always be present. Such gaps should never be considered a validation for a negative argument. That’s just a logical fallacy and a trap for the naïve.The above mentioned video of Ken Miller covers all of this nicely. https://www.youtube.com/watch?v=04XL1Li0dI8 I’m not really sure why “atheists” are the ones tasked to counter your position. Personal philosophy really does not have anything to do with science, unless it clouds one’s ability to do it properly and this can happen regardless of one’s philosophical position.

        -Codes. I am not in any way qualified to tackle you on the matter of codes, be they your asserted “fundamental property in biology” or that “all codes we know of have been designed”. Definitions would be important here, especially in order to prevent equivocations and conflations based on simply using the word “code” and thinking we are always talking about the same thing. I find the statements here to be a little confusing, even a little circular, however I suspect that the latter refers to human world constructed code in engineering. Well this is, by definition, designed by our naturalistic intelligence. I do hope that this does not form the basis of “proof by analogy” into the biological world. If your “biological code” is naturalistic (but not due to the evolutionary theory) then I’d be really keen to know what this is. If this “fundamental property in biology” is supernatural then we have drifted away from scientific examination and firmly into the land of philosophical conjecture, indeed religion. I have elsewhere discussed the inadequacy of inference to an untestable “explanation” and thinking that this is where science “down tools and takes a coffee break”. In any case I can see how your “code centric” analysis of the DNA sequencing has resulted in your misunderstanding (mis representing) the statistics of random mutations as described by your “google ad random generator” and its “golden nugget” approach to “successful” combinations as discussed above. I am not a statistician however, because you present in the public space and appear to be an intelligent and sincere person, I really do recommend that you consult with some one who can best explain to you the basics of population statistics. Yes yes, they will tell you to drop your “code centric” analysis of DNA sequencing and its failed “random generator” slot machine thingo what ever. In its place they will likely suggest that you give serious consideration to the “phenotype driven” analysis of DNA sequencing which does not require said “golden nuggets” to “win” the combination prize. Of course this will infer the dreaded naturalistic explanation. But surely, if the statistical analysis stacks up then this is what science is all about isn’t it? A testable naturalistic explanation that is backed by the vast statistical analysis of population studies. Phew, can it get any better than that? God loves the way science works to explore and examine his handy work.

        -“All codes we know the origin of are designed.” I presume you are referring to human designed engineering codes here. “This infers design in biology”. This is just a baseless assertion. “That’s a fact.” Emphatically claiming it to be a fact is just hubris.

        -“Nobody has ever shown us how to get a code without designing one. This doesn’t prove God. The problem may very well be be solvable. I hope it is. If it is solved, it doesn’t disprove God.” Yes, proof and disproof of God are both left off the menu, well written. However, you write that “the problem may very well be solvable”? Science doesn’t solve things, that’s maths, science provides “best and latest natural explanations”. But Perry, you have claimed elsewhere that your code theory has already provided proof of God’s existence, so doesn’t this end the enquiry? Or is this “pending God” only creating code while we “haven’t solved it”? Please excuse me here Perry, I’m really not trying to be smart but I am just not getting any of this.

        -“And it still leaves us the question of where it all came from.” Philosophical conjecture is to be encouraged, but not in the science lab.

        -“I am at odds with the Intelligent Design guys because, as you point out, they vaguely refer to design in biology and then act as though this solves the problem. Well in their mind it settles the metaphysical problem but it still doesn’t answer the scientific or technological questions. And the way *some* people (but not all) apply ID, ID becomes a science stopper pure and simple because inquiry stops.” I suspect a serious case of pot calling kettle black syndrome going on here Perry. I’m serious.

        -“I was dissatisfied with that. Why? Because I’m an engineer. Scientists cannot say “God did it, that settles it, let’s go out for a 3 martini lunch.” Neither can engineers. So ID comes up short.” I want to be honest here Perry but the only difference I see between the ID God and yours is that yours appears to be some sort of “pending God”, the one who beavers away on his biological code until some smart human scientist catches him out.

        -“I was equally unhappy with the likes of Richard Dawkins saying “life was a happy chemical accident.” Did my mate Rich really say that? hmm, I’d like to know the context but in the meantime, we don’t have a compelling theory of abiogenesis so I really don’t understand this. I observe that he really does have a dry sense of humour, but before you accuse me of just letting an atheist off the hook, I’ll just get off the bus here while I think I can.

        -“I do not believe there is any one place where you step across a dotted line and say “OK, THAT is God!! There’s the proof, right there!” Phew, I do wish you’d be consistent then Perry. OK, so I’ll now take that as that you do not have proof of God and any inference to that is mere heresay and I got it all wrong then. So now you can focus on your prize for that naturalistic explanation for your putative “code”. Good luck with that, but unless you get rid of your slot machine style “golden nugget” generator I really don’t think that a Nobel Prize will be in the offing. But I suppose such a thing is not to your fancy then.

        -“Echoing Denis Noble, I also don’t believe there is any privileged level of causation in biology.” Just that testable natural explanations trump supernatural inference. He uses the word “privilege” here. Do I suspect an ‘establishment conspiracy” going on here?

        -“My hunch is that nature is “turtles all the way down” where you never reach the end of the complexity and the layers.” Sounds like philosophical conjecture to me. Nothing wrong with that, I too wonder about the end to the infinite regress, but never “in the lab”.

        -“The closest you can get to logical proof of God, in my opinion, is Godel’s incompleteness theorem. What it says is that if the universe is rational and logical, then there is necessarily an infinite boundless entity outside of space and time which is responsible for it.” As previously discussed, I happily read your articled on this and found it interesting. I don’t know how much theological re interp can be put onto what was essentially a mathematical proof of the limits of knowledge (mathematical proof is not proof of a supernatural concept, certainly not one with any socio-cultural-political agenda, such as religious Gods) but it reminds me of the philosophically based Leibnitz Argument from Contingency. I do find the notion of an essential cause for the contingent natural universe to be philosophically plausible. However, as I mentioned elsewhere, I stop at describing it as an inexplicable “Absurdity” and then leave it at that. For me, the rest of my world becomes so much more coherent when I have this as my starting point. But that’s just me.

        -“And if there is not such an entity, then the universe cannot be rational and logical but rather exists for entirely illogical reasons. It perhaps popped out of nothing for no reason at all like Lawrence Krauss claims.” eeerh, well, the Universe undoubtedly exists and it is undoubtedly rational and logical even if you claim this is for “entirely illogical reasons”. Personally I think that asking “why” the Universe exists is just a silly question, silly because it is basically unanswerable. I prefer to think about questions that can be answered and admittedly these are “how” questions. OK so that’s a little dry isn’t it. I find that “why” questions that can not be answered tend to have more of the quality of enabling the person who asks the question to validate his world view. In the Australian parliament they have this term about “Dorothy Dixers”, when politicians ask questions just so they allow their colleagues to answer them. They are simply a prompt. Lawrence Krauss claims to have an explanation of a universe from nothing. Yes there is a lot of problems with that, I suspect the heading is designed (yes, designed) by the publisher to be catchy. Krauss speaks of quantum vacuum states going into and out of existence like the fist/hand opening and clenching. So follows the question of whether this be truly “Nothing into Something” or just “Two states of Something”. I think the latter. With Leibnitz in mind, I’m inclined to go back a little further into the infinite regress into the true “Nothing” of the philosophically essential first cause, my previously defined “inexplicable absurdity”. The fist/hand analogy I would give here is one of a closing and opening fist that the owner hides behind his back.

        -“Thus if God exists, science is valid. If God does not exist, science is not valid, because the universe is necessarily inconsistent and therefore not compatible with all scientific presuppositions.” Not so fast there eddie. The Naturalistic Universe undoubtedly exists, that’s why science works. All else is philosophy, conjecture and assertion.The western philosophical tradition conjectured our universe is rational, intelligible, consistent, law bound, closed causal and that there was an explanation for this and that this explanation had to be external to this Universe. By the time of Scholasticism the Christian world was beginning to fully embrace its western philosophical roots and incorporated this notion into its theology whereas it seems that the eastern traditions had it that this world is, itself, divine. Good on them both, but I think the Christian West “won” that battle thanks to its philosophical roots. Well that’s my “couch theology” appraisal. I’m the universal layman in my own lunchtime and always “permanently provisional” in my thinking.

        -“You cannot prove this one way or the other.” Too right. “I can only point out that you can’t have your cake and eat it too. You can have God and science; or you can have an irrational universe. There is no other choice.” Phew, no other choice. So on the one hand you correctly claim that we can not “prove this one way of the other”, but then follow up with numerous baseless and emphatic assertions concluding with the totalitarian “no other choice”. I am happy to say that I find the notion of an external and essential explanation for the contingent naturalistic universe to be philosophically plausible, however all we know for sure is that the Universe is naturalistic and that this is why science works. The inexplicable absurdity is where my infinite regress presently stops. My sense of a notional God with all of its anthropomorphic qualities is that this is symptomatic of the natural world phenomenon of religion.

        -OK so you still emphatically insist that “the neo Darwinian synthesis is dead”. Sounds so over the top to me, but we’ve been there, done that. Looks like this chap Denis Noble is your go to man for this. Perhaps he is an interesting cage rattler in the science of evolutionary biology, why not? For now, I’ll be guided by the permanently provisional consensus, as always, and try not to jump the gun (or the shark?) with strongly held pet hypotheses.

        -in all of this discussion, I am personally not fussed about personal philosophies or religious beliefs, atheistic or otherwise. My desire is to fully understand the way that we examine the natural world. What one believes is beyond, behind, above all of the workings of this world and how or if it interacts with it is interesting too but beyond the scope of this discussion. But I don’t believe this need interfere with our understanding of how we examine the natural world.

  5. John Lyster says:

    PS. For the scientist studying naturalism in the lab……………….

    -God, or its absence, is irrelevant

    -Atheism is intellectually untenable (it is not possible to provide a positive argument to prove an absence, there are no negative arguments against the existence of a supernatural entity, it is not possible to find a naturalistic explanation of the supernatural and the certainty demanded of this position is a statistical impossibility)

    -A-theism is mandatory (for the naturalist mindset working to methodological materialism one must presume that interventionist, personal theities don’t exist)

    For this reason, the new-Atheists provide an excellent intellectual framework for the scientist studying naturalism in the lab. If there is to be any Kuhnsian shift to a more rigorous and workable science, it should come from this direction.

    Outside of the lab, all philosophical and religious positions regarding the supernatural are one’s own business.

    Personally I would define…………

    -Natural; law bound, rational (uniform and consistent in time and space), intelligible, universal, simple, closed causal. The Universe that is open to scientific examination. Philosophical considerations. Is this truly an existence and reality or is it a human constructed, bounded set of conditions that “works”? Did we discover this or did we invent this for our purposes? Is this all there is or is it just “the internal Universe” bounded by an inexplicable Absurdity/God?

    Beyond and external to this…………the Universe that is beyond the scope of scientific examination. The existence of such as an essential entity (source of its own causology), that being the first cause and prime mover of the contingent (natural) universe, the end to the infinite regress, is pure philosophical speculation. All inputs gratefully received.

    -Supernatural; the philosophical concept of a personal, interventionist, natural world entering, religiously defined, anthropomorphised God for which there can be, by definition, no naturalistic evidence, hence beyond the purview of science. At this time, I rate this low, I consider religion to be a naturalistic phenomenon of human nature and its efforts to anthropomorphise this entity a characteristic of our human nature and attempts to overcome existential angst and make sense of the ultimate absurdity that is our sentience……..but everything is permanently provisional.

    -Non-natural; the philosophical concept of an impersonal, non interventionist, natural world non entering, inexplicable absurdity for which there can be, by definition, no naturalistic evidence, hence beyond the purview of science. At this time, I rate this high, its seems to make my world coherent……..but everything is permanently provisional.

  6. John Lyster says:

    Perry, you have deleted my last comments. OK so they were very long. Was there any problem there apart from this please? regards

  7. John Lyster says:

    OK, back again, Friday afternoon here now and terribly hot, so relaxing in front of this screen and reading through some of your comments above.
    1) Much is made of this desire to re-conciliate science and religion in order to accommodate the urgency indeed, dare I say it, anxiety about people retaining their faith. Well I have my thoughts on the psychology of all this, but specifically, I think if you could spare the time and energy to read through my comments above then you would see, from my perspective anyway, that science ain’t going to do anything to upset God based belief systems, no matter what it successfully explores (“scientists don’t think enough about God to know if they are atheists or not”). That’s not to say that I believe in the “overlapping magisterium” which equates but separates these ontologies into their respective spheres (personally, I do not rate religion as highly as science and pure philosophy…..but that’s just me). One can examine the natural world completely irrespective of one’s faith or non faith orientation. BY DEFINITION, science does not do God. Science does the natural and God is supernatural. The bone of contention is the naturalistic claims made by religion, yes things like the virgin birth or miracles. Hence science does pose an issue for religions that do this, but even then the Catholic Church straddles the middle ground with it’s more philosophical, as opposed to scientific, approach to this matter. They have sophisticated philosophers and main stream scientists on their books and much European history to work out where they stand (eg, transubstantiation of the “host” is a an “Aristotelian Accident”.) Far be it for me to try to convert you to Catholicism lol, I am merely pointing out that the Church has a belief system that incorporates the supernatural acting within the natural and the main issue is that this is an issue of philosophy, not in any way a scientific issue. I think that this approach allows science to get on with this job and the Church simply looks on in appreciation. No threats, no anxieties. I say, “outside of the lab, all philosophical bets are off, but inside the lab, let’s stick to the job at hand……the search for natural explanations”. 2) You make much of the “end of NeoDarwinian synthesis” with especially emphatic claims. I would make two observations here if I may. i) I suspect that you psychologically “have it in” for neoDarwinism because you see it as some sort of subversive materialist plot to get rid of God. ID people are quite overt about this. By my reasoning, may I suggest that a complete naturalistic explanation of life, along the lines of Standard Evolution Theory, poses no concerns to any particular faith orientation. On the other hand, may I respectfully suggest that you appreciation of the science is being affected by your belief system, one that appears to believe that science can somehow “prove or disprove” God (that’s my “couch psychology” working for you). ii) I looked around a little at your information re these people who are proposing this big game changer in evolutionary theory, eg Denis Noble. These people may well be highly qualified scientists, they may even be onto something, far be it for me to say. However they are still in the early days as far as having an effect on the present scientific consensus. The consensus on neoDarwinian synthesis has been slowly building up for 150+ years and its edifice is not about to fall quite so quickly. This is the nature of scientific consensus. Unless there is a clear point of falsification then it’s the endless process of refinements and fine tuning. You will no doubt consider that such falsification has been reached, or at the very least their new ideas are a different but more powerful theory that should replace the present one. Personally, I simply say, “not so fast eddie” and I will continue to follow the ever evolving consensus as presented by the reputable scientific bodies, academies and institutes in their “position statements”. I see strong parallels here with the approach adopted by climate change sceptics (OK so we should all be sceptics). I consider the people you have sourced here to be mavericks AT THIS POINT IN TIME and I simply await the scientific consensus to yield to them if they do happen to be “on the money”. Then the Nobel Prizes will follow.

    • “Unless there is a clear point of falsification then it’s the endless process of refinements and fine tuning.”

      There are numerous VERY clear points of falsification. This is why Stephen Jay Gould said Neo Darwinism was dead as long ago as the 1980s. It was true then and it’s even more true now. Read one or several of the sources I cited and then I will be happy to engage with you about this.

      • John Lyster says:

        I am aware that the modern evolutionary synthesis is under review, such is how science works, “permanently provisional” as the consensus is under permanent challenge. I am also aware of the work of Stephen J Gould, his general perspectives on this synthesis and his extra curricula commentaries on the relationship between science and religion. I am aware that he was highly regarded as a high profile public educator of the sciences in a very general sense, and that he contributed to the usual “debates on issues” within science and “challenges to the consensus” however, from what I have read, I do not consider that his work, or the work of the others that you have quoted, has in any way “falsified” or rendered “dead” the modern evolutionary synthesis. I think we should be wary of cherry picking or over assessing the significance of individual quotes of highly qualified people, particularly when they speak or write outside of the formal scientific peer review. For the overall scientific consensus I default to the positions adopted by the mainstream scientific bodies and academies. That is not to say that the present consensus is static, both now or into the future. For me to accept the individual and non contextual quotes of Stephen Gould or Denis Noble on the matter of the modern evolutionary synthesis in this way would be as inappropriate as my accepting individual commentaries from Richard Dawkins on his “selfish gene” proposal as representing the consensus. As I wrote elsewhere, I consider Dawkins’ concept as a very good communication device but it is not science. Like you, I am interested their extra curricula commentaries, but when these people do this they are not speaking within the scientific peer review and neither represent “the consensus” as this is simply not how science works. I read your cited articles and to me the proposal of an organism or cell based “goal directed” real time evolution working by the processes such as you include in your “swiss army knife” is interesting, if not dangerously close to “intelligence directed” evolution that you have more openly canvassed yourself (let’s not equivocate the word “goal”, or some such physiologically based “natural purposiveness”, between natural and supernatural shall we? In science, “agency in evolution” must always be naturalistic, by definition). For this to be a naturalistic mechanism then they must be inferring, at the very least, these multi level feedback processes that appears to be Denis Noble’s thing or perhaps (at best) some sort of low level neurologically based mechanism within very low level cells. I have seen reports of this sort of thing before, like some sort of low level reflex mechanism going on, such as we also have in our lower brains, or perhaps some sort of chemical based reflex system. But to infer that this is some sort of sentience would have to require further evidence and I certainly don’t have my head around that one. I guess this all goes to “when does sentience or consciousness emerge” in living tissue and of course, in principle, this is a very interesting question indeed? Similar to “do animals experience pain like humans do?”. Of course, even if there is some level of sentience going on here then this must be naturalistic and simply leaves the concept of a putative supernatural intelligence guiding it back to the philosophical infinite regress in the same way as our own sentience. Well good luck with this project but I don’t think this renders the present consensus “dead”……not yet. I notice that Denis Noble is a specialist in physiology rather than evolutionary biology. This doesn’t eliminate his proposals from the consensus, however I would suggest that it gives a sense of where he is coming from on these questions. Perhaps that is a good thing but one, of a small group of proponents, however interesting, does not a dead neo Darwinian synthesis make. Not so fast eddie lol.

        (I notice the discussion of Dawkins’ weasel program in the Denis and Raymond Noble article and quote, “Evolution is a high-level forming process, not simply a matter of genome informatics.” May I propose that you reconsider your “slot machine” style random generator analogy in the light of this discussion.)

        Quote from two books that Gould wrote in 1980-82 (and another from 1988); “The challenges mentioned above are seen by some scientists and evolutionary historians as a severe test of neo-Darwinism, concluding that “there is no longer a universal consensus in favor of the synthetic theory” (Bowler 1988), or that the theory has broken down on its fundamental claims and thus, “if Mayr’s characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its textbook orthodoxy” (Gould 1980, 1982).”

        Quote from Gould’s final book just before his death in 2002. “However, what some see as threats to the modern synthesis, others see as theories that can be included within the umbrella of a broader, more pluralistic modern synthesis (Gould 2002).”

        Both (and Bower’s) of these are non peer reviewed commentaries or opinion pieces and neither formed the basis of the scientific consensus at the time they were written, however it looks like Gould softened his position towards the end of his life. Perhaps he mellowed his youthful exuberance.

  8. John Lyster says:

    OK, I do hope that I am not driving you nuts with all of my commentary but I’m trying to come to a position that I think fairly accommodates all the different assessments going on here. I’ll now cease and desist this relentless affray as I think I’ve had enough…….for now. Perhaps I have nothing better to do as I seek shady relief from sweltering in over 37C heat in our mid summer (and getting hotter over the next few weeks) as I notice that your city dips to a “global warming” cool of -15C.

    -May I define…….

    a) Atheism (pronounced atheism with a quick “a”): The positive/strong/assertive claim that there is nothing beyond the natural. I have discussed above why this is an untenable logical position to adopt in the lab, not the least because “nothing is certain”, one can not “prove a negative” etc and of course this is actually a claim about the supernatural, something that is simply of no interest to science (as Steven Weinberg put it so nicely and succinctly) even if it could somehow be “proved”. It is only possible to adopt this as a philosophical position outside of the lab, the philosophical materialist. Personally, I do not find this to be a philosophically plausible position to hold…for now.

    b) A-theism (pronounced aah-THEism with a long “a” and emphasised THE): The negative/weak/reservist acknowledgement that there is simply a lack of NATURALISTIC evidence of the supernatural in our world, indeed there can not be…..BY DEFINITION. I have discussed above why this is the proper “scientific mindset” to adopt in the lab, methodological materialism. Inside the lab, this is not a philosophical position that one has, this is simply a “scientific mindset” that one adopts in order to do good science THAT WORKS. Outside of the lab, this simply becomes a matter of semantics and what one means by “evidence” as this term now becomes philosophical (eg Catholic Church term of “Aristotelian Accidents” is a long way from naturalistic evidence). Boy have I noticed so much confusion, conflation and obfuscation on this very point. I’m happy to think of myself as a philosophical “A-theist”, however this is not something I would trumpet because of all the confusion and emotion that goes on about this term. For me, a case of, “who can be bothered?” in a social setting, but it’s a different thing in a respectful internet blog such as this. While I have a sense of the philosophical Absurdity as the essential first cause, because I consider it to be inexplicable I think of my position as a sort of logically deduced agnosticism (as opposed to the intellectually lazy, “I don’t know and I don’t care” of most people). Personally, I find this to be a more philosophically plausible position to hold….for now.

    At the core of all of this confusion is, I feel, the very issue of the naturalistic claims of religion, the definitions of evidence and the philosophical positions held about the way, or if, supernaturalism interacts with naturalism. For some this is a very direct and personal interaction, for others this is some sort of behind the scenes ever presence. For me, this is way back in the infinite regress, along the lines of the Leibnitz Argument for Contingency. It’s what I define as the philosophical “Non-natural”, so as to delineate it from any sense of the direct supernatural presence within our natural world and its conflation with naturalism.

    No value judgement should be interpreted on the labels “positive/negative/strong/weak/assertive/reservist”, I am just trying to define my terms in a logical manner here.

    -From this above discussion, I would like to make the following observations for your interest.

    -Richard Dawkins carries his excellent “scientific mindset” too much into his personal philosophy. In the lab, he is EXPECTED to be an “A-theist”, what he does in his “spare time” (now that he is a socio-political commentator and not a scientist) is up to him. Personally I think that “Atheism” is an untenable philosophical position to adopt, but of course “outside the lab” he is perfectly entitled to what ever position he wants. But please don’t bring pure science into your socio-political advocacies. Sometimes I think that Dawkins thinks he is permanently “in the lab” and the world is just one big experiment. I think this makes him an excellent scientist but not such a great philosopher. I think his beef is much more of a socio-cultural issue with religions than a truly coherent philosophical problem with “God”. He seems to acknowledge this when he speaks of himself as being “6.9 out of 7 on the atheism scale” and he has even suggested his bold and emphatic push for Atheism is very much about creating a strong political impact. I do feel that there is a lack of nuance going on here, perhaps that is just his personality style. The trouble now is that he is firmly pressed into his self created corner and any “admission” towards nuance would get “crucified” out there in his much beloved political sphere. I sense that Sam Harris might feel a similar way to me on this point and have more nuance and subtlety in his approach. My sense of Christopher Hitchins is that he was just “up for the fight” because he was just so good at it. Give him “final victory” and he would have been miserable because the art of debating and intellectual challenge was his raison d’etre. As the Monty Python people of England would say, “he was in the room for an argument”. I sense that Lawrence Krauss is just the pure scientist through and through, very much in the Steven Weinberg “doesn’t think enough about God to know if he is an atheist” mode, but has just gone along with the Dawkins project because they have become such good mates. Dawkins and Krauss don’t appear to have much regard for the philosophical project and I think this shows when they “leave the lab”. Krauss’ assertion of the “universe from nothing” seems to carry all those hallmarks. As philosophers, these two chaps seem to make very good scientists (but I think Sam Harris is a little different).

    -If you don’t mind my saying so, I think that you suffer from the reverse “problem” to Dawkins in that you carry your religion into the lab too much. From all that I have written above, may I boldly recommend that you “think like an A-theist when you are in the lab”. Who knows, you may even begin to “love” the “scientific mindset” of someone like Dawkins even if you abhor his philosophy and personal style lol. For me, “God” is a purely philosophical concept, however when I read through your commentaries I get the sense of you as an engineer and a religious person who believes in the direct supernatural presence and MUST “prove his God” in order not to lose his science or his religion. In this way then, I get this sense that you see God as this gigantic celestial lab technician, tinkering away on “his code” in exactly the same way as us natural world intelligences do so in Information Technology. I feel that this is an equivocation of two entirely different things, the natural and the supernatural, simply because of the use of the same words, code, intelligence, design. You are the successful engineer who is looking for supernatural code in exactly the same way as you look for natural code in computer software. I think this thinking goes to your consideration of what I have called, “the pending God”, a sort of lab technician who has provided us with his secret code while he is at work, but soon knocks off or takes a back seat when some smart chap discovers your holy grail of naturalistic evidence and takes home your prize. If there is a supernatural entity “behind this code” then this can ONLY ever be a philosophical concept for which there can be no discovery “within the lab”. In the meantime, we either have a naturalistic explanation (I think we do have that with standard evolution theory) or “we don’t know”. I think this sort of thing, God as the lab technician, hits its “zenith” with Michael Behe’s bacterial flagellum. I think this is a preposterous concept that is the most unashamedly unscientific proposal put forward by the ID people. Ken Miller (the Brown Uni Professor in the linked video I put up above) has an excellent evisceration of this nonsense with his “mouse trap” analogy. I think that this “God is a lab technician” approach reduces and demeans the concept of the supernatural almighty into a silly jingoistic argument in order to further a socio-political agenda for vast numbers of the unsuspecting. How, very political.

    -There is a term NOMA (Stephen J Gould, “Non overlapping magisterium”) that you are probably familiar with. The notion that there are three separate and equal ontologies of science, philosophy and religion, each going about their respective tasks within their own spheres. For my part, I believe the project of ontology is to progress our understanding of our Universe with a purely open mind from the blank space (tabular rasa if you will). I believe that the projects of science and philosophy do this, however the project of religion essentially begins with its answer and then expends all of its energies reverse validating, justifying and rationalising this position. In this way, European Christianity spent approximately the first millennium CE in spiritual “Monasticism”, not really unlike the pantheism of eastern religion, before it accommodated formal philosophical concepts and entered the era of “Scholasticism”. For my part, science and the study of naturalism (and all of its benefits and problems) evolved out of the European philosophical tradition with Christian religion in a sort of parallel universe. Of course the adoption of scholastic principles by the giants of Christianity, such as Thomas Aquinas, created the cultural milieu and intellectual framework within which science was born and flourished, however I do not think this occurred from a purely religious perspective. Without European Philosophy, my sense is that Christianity would have remained in a state of mysticism, not unlike what remained in the east. Personally, I think of there being two NOMA and religion existing as a naturalistic phenomenon in parallel to science and philosophy. Well, that’s my overall “couch historian” perspective, I do hope your blood pressure has not been too elevated.

    -Some further reflection on what I’ve previously written………….

    -I made the observation that ID is not falsifiable (as you agree), but that your idea of “code centred” evolution is putatively falsifiable by someone coming up with an acceptable (to you and your committee) naturalistic mechanism. Actually I now take this back. The only way that your “code centred” evolution can be falsified is if it provides a testable mechanism which is ITSELF falsified. Scientific hypotheses are not falsified by other hypotheses doing better, they must swim (positive arguments….see Ken Miller video) or sink on their own recognisance. Because you infer a supernatural agency to your “code” then your proposal/assertion is itself not falsifiable, regardless of whether there is an acceptable “alternative” naturalistic hypothesis. If your proposal did provide a testable mechanism then of course it may be replaced or upgraded by a competing hypothesis that is more broadly explanatory, simple and compelling in the same way that Newtonian Classical Mechanics has been upgraded to Einstein Relativity but not falsified by it. Without a testable and INTRINSICALLY falsifiable mechanism, your proposed inference is “not even wrong” as they say. I really can not see much difference between your proposal (not hypothesis) and ID, except I note that you seem to argue that your “code” expresses itself through this “swiss army knife” idea.

    -I’m not sure what you make of my labelling your proposal as “code centred”. By this I mean, the genes have this “God given” code and then all else follows. This is to be compared to the “external to gene” approach of neoDarwinism, that I would consider to be due to the one, two stage, mechanism of “randolection” (or what ever one might call it……..hmmm, sounds like the proverbial “crocaduck” does it not? lol). This is to be contrasted to the two separate mechanisms of random mutation and natural selection (that I consider results in too much emphasis being focused on “ungodly random” and “deleterious “mutations” on the one hand and the “universal, answer to all things, driving force of natural selection” on the other). This “code centred” label of mine should not be confused with Richard Dawkins’ “selfish gene” label which appears to sound decidedly similar. By “code centred”, I am attempting to create a label that helps me to simply “nut shell” what I think you are proposing in comparison to the standard evolutionary model. I view Dawkins’ “selfish gene” label as merely an educational analogy that explains the concept of standard evolution as a mechanism that, IN EFFECT, protects the permanent existence of the DNA molecules in an ever changing environment. In this way, the molecule requires the death of its host (poor old us) in order to, itself, become “immortal”. I don’t view this as some sort of emphatic claim of the nature of reality, or a scientific hypotheses to be proposed at a scientific meeting (heaven help Dawkins if he ever did that). I view it as an excellent piece of educational conceptualisation in order to better communicate and nothing more. “Selfish” does not have an operational definition to “test”. Even Richard Dawkins is allowed to anthropomorphise the natural world, but he is not being literal here when he refers to the gene as “selfish”. There’s been so much nonsense interpreted about his use of the word “selfish” but I’m sure he and his publishers are happy about the book sales, especially after striking gold with that “God Delusion” title. Not unlike the mis understanding and mis representation of “survival of the fittest” over the years.

    -while on this issue of analogies, you wrote, “All codes we know the origin of are designed. This infers design in biology. That’s a fact. Nobody has ever shown us how to get a code without designing one.” I consider this to be a serious case of attempted “proof by analogy”, one of many fallacies that has no place in scientific (or legal)reasoning, along with the “GOG” fallacy. I am certainly not qualified to dispute your claim that biological code is, in some way, synonymous with the human created code of Information Technology, this is presumably an arcane area of expertise that I do not have my disposal. However, I think you have clearly “jumped the shark” when you attempt to make the analogy of what we know to be human intelligence (naturalistic and testable with its footprint) code with your proposed supernatural intelligence code in biology (no testable footprint). May I propose the following restatement of what you have written here. “All codes in the human intelligence world of Information Technology have been naturalistically designed. These codes share many characteristics with the biological code of DNA (??? I am merely conceding this in order to progress this discussion). This infers naturalistic design in biology. But we don’t know this as a fact. We need to continue our search for a compelling naturalistic explanation for this code, one that we can test”. Inference (just like analogy) is not a fact, it is merely the opening gambit in the inductive/deductive cycle of the scientific method. Analogies are merely communication tools.

    -You wrote, “Based code not being an analogy, but code being a fundamental property of biology. We’ve all known this since the 1950s.” Again, I am not qualified to counter your discussions on the technicalities of “code”. Perhaps (presumably) the codes of naturalistic world, human intelligence created, Information Technology are perfectly analogous to a naturalistically created “biological code”. The job is then to either admit that we do not yet know what the naturalistic mechanism for biological code is and to keep searching for it. Or to at least pronounce the mechanism of neoDarwinism as the present “best we have but we think we can do better” (as I suspect is the approach of people like Ruse and Nobel). It can never be acceptable to default to the supernatural inference and then “settle for the 3 martini lunch” as you would have the ID people believe, yet seem to be simply doing a variation of yourself with your “pending God” proposal. I think I’m beginning to see where you have “got into bed” with people who are not really on the same page as your good self. I now see that they are into a “better naturalistic” hypothesis than neoDarwinism (so they think), but this is not where you seem to be coming from. I suspect you may need to have some deep and penetrating chats with them. In this way then, I again challenge the notion that neoDarwinism has been falsified (pronounced “dead” as you have put it). Further refined by this “extended” hypothesis, perhaps, even superseded by this theory that is found to be more broadly and efficiently (Occam’s Razor) explanatory, maybe? But hypotheses sink or swim on their own account, it doesn’t take other proposals to falsify it, except when bombastic language becomes the norm. In the meanwhile, as I have previously written, I’ll just let the scientists do what they do and I’ll follow the “permanently provisional” consensus to where ever it goes.

    -I have briefly touched on your discussion of the “Gödel Incompleteness Theorem”. This is, strictly speaking, a mathematical proof about the limits of knowledge and while I consider your discussion to be an interesting theologically based re interpretation, I am really not sure that it can stack up as the definitive proof that you appear to claim/desire. I will reserve judgement on any philosophical inferences that can be drawn from this but I really have only read your discussion piece on this matter. When I first heard of the Heisenberg Uncertainty Principle at high school, I made my own personal “theological” deductions and it all it did was to lead me away from the “certainties” of religion. I think these things can be interesting discussion pieces but I would always urge measure and circumspection on drawing long bows and conclusions from naturalism to supernaturalism. The Leibnitz Argument from Contingency is philosophically based and so I think it is a more compelling and acceptable starting point for considering what may lie beyond the natural world.

    -I have previously discussed your analysis of the google ad “random code generator” and my assessment of it as simply a slot machine looking for a “golden nugget” combination that “wins the lottery”. After some consideration, I can actually see that you would interpret the process of evolution along these lines because you are viewing the mechanism of neo-Darwinian Evolution as attempting to fulfil your “Code Centric” proposal. No wonder it fails when applied to the neoDarwinian Synthesis. Either this is a mis understanding or perhaps even a deliberate mis representation (as I am absolutely is certain goes on out there). The explanation of the way that “code generation” occurs according to neo-Darwinism is covered by the much more sophisticated analysis of population statistics as I briefly mentioned above. This would include analysis of point mutations (as your “slot machine” does) but also gene copying “errors” (evolution only works because of such errors of replication….perhaps it could be philosophically argued that the almighty had this in mind as his “preferred mechanism”?), not to mention all of the matters discussed by your “swiss army knife” mechanisms and more. Yes, I suppose that people like Denis Noble believe they have a better way to explain what is going on than the present synthesis, but if they are true scientists then I presume their explanations are always going to be Natural. I have only a very general appreciation of all this statistical analysis, but far from debunking the standard evolutionary hypothesis I think that your “slot machine” only invalidates your own “code centric” proposal, or it is simply an inadequate analogy to explain anything but a night in Las Vegas. Your call.

    -I’ve seen and read a little by Michael Ruse and he certainly provides some interesting pushback on people like Richard Dawkins and I rate him highly…..so far. Considering my now growing analysis of your proposal (yes, proposal…..not hypothesis) I really am now wondering about his motivations in getting involved with your “competition”. Yes, I’d certainly find his motivations and thinking on this matter to be interesting, it could share some light on my own perspectives or possibly be a cause for me to “downgrade” him in my ratings scale. Hard to know from this distance. I notice that one Paul Davies has also been involved in your efforts, he was once in the employ of my alma mater. I know that he has a strong involvement in this science/philosophy/religion business and I believe he has been involved with this Templeton Foundation, something that Dawkins rails against. I suspect he is more science/philosophy and less religion, which is of course the Michael Ruse perspective (this probably suggests why they are both involved with this project). Perhaps there is some sort of symbiotic relationship going on here where all of these people are using your entrepreneurial and marketing skills to promote their “naturalistic” update/replacement of the present Evolutionary synthesis (with a little help from the general public) and you are happy to have some sort of scientific cred implied to your own pet theory and book sales. Everyone’s motivations are each to their own.

    • Most of your questions are answered in Evolution 2.0.

      Read it. Spend the money and spend the time. If you won’t, I won’t engage with you.

      Ten years ago I would and did engage with any halfway reasonable person with any halfway reasonable question.

      I answered tens of thousands of emails – literally any civil person who replied to me from an email list of 275,000 people. And then, for the last 5+ years, to people on this blog.

      I have done that now long enough. I have also invested thousands of hours writing a book and organizing a prize, which is endorsed by some of the most eminent evolutionary scientists and professors in the world from Oxford, Harvard, MIT, UCLA, Notre Dame, King’s College; editors of several major biology journals, and other institutions. They have written their own books as well.

      If you want my time and attention, and if your questions are sincere, you will be willing to invest the money and the time to read what I have written. I don’t have time to re-state it here.

      (You can also find the answers to most of your questions on this site in the articles and comments.)

      Skin in the game. Your questions must show familiarity with my work.

      I am extremely busy; I am a highly sought after person, as one of the highest paid business consultants in the country and I am notable in four professions: acoustics; process control engineering (wrote an Ethernet book), business strategy, and evolutionary biology.

      The opportunity cost to write Evolution 2.0 was millions of dollars for me. Believe me, I could have made far more money doing something else.

      Furthermore, numerous very wealthy people have committed millions of dollars to the Evolution 2.0 Prize. The science and logic behind it has been refined now for 13 years. Almost all of that history is on this blog for all to see, which has over 10,000 comments.

      From this point forward I will freely engage only those who will fully engage with my work. I have earned the right to say that.

      Evolution 2.0 is well worth your time. Put some skin in the game. Read the book from cover to cover (including the appendices) and then come back with your questions. I will similarly engage with people who have read books like:

      Dance to the Tune of Life: Biological Relativity by Denis Noble
      COSMOSAPIENS by John Hands
      Evolution: A View from the 21st Century by James Shapiro
      Purpose and Desire by J. Scott Turner
      Acquiring Genomes by Lynn Margulis and Dorion Sagan
      Symbiogenesis: A New Theory of Evolution by Boris Kozo-Polyanski, Lynn Margulis and Victor Fet
      Recordings and papers from the 2016 Royal Society Evolution Meeting
      Historical Genesis from Adam to Abraham by Richard J Fisher

      That is my New Years Resolution for 2018 and it applies to everyone.

      • John Lyster says:

        OK, I take on board all you have written above Perry and can see that we can leave it at that……for now. I did read your above mentioned citations and I found them to be interesting and I included directed observations in my reply above. Please excuse me if this looks like I have been, in some ways, proselytising my own point of view, however I have done so in direct response to what I have read on your site as I have found some of your thinking to be confusing, well at least from my perspective anyway. I do hope that you have taken my comments to be in the spirit of positive challenge although I accept that my comments on your intentions with the prize were a little edgy. I mean no disrespect. One last summary of my present position below before I sign off……for now. cheers jl

        -The job of science and scientists is to search for naturalistic explanations of observed phenomena without philosophical fear or favour. For this he must adopt the A-theistic, scientific mindset of methodological materialism. He does this, not because this is necessarily all there is, but because it works.

        -Outside the lab, the scientist may adopt any philosophical position, including religious supernaturalism or Atheistic philosophical materialism.

        -Apart from the work of social and natural sciences in our everyday lives, there are likely three outstanding grand projects for the natural sciences in the relentless pursuit of naturalistic explanations for the observed phenomena in our Universe while giving no regard to the bias of personal philosophies, convictions, belief systems or world views. Philosophical supernaturalism or non-naturalism has a place outside of the lab, not within it.

        a) Origins: There is no acceptable model of quantum gravity (the large crunched into the small) that can satisfactorily examine and explain the supposed singularity of the “Big Bang” some 13.7 billion years ago. The best theory we have at the moment is “String Theory”. The present Standard Model of Cosmology can look directly back to the time of the Recombination Event at the purported age of ~380,000 years after the proposed “Big Bang”. This is when the expanding Universe cooled sufficiently for the electrons to recombine with their protons and change from the hot opaque plasma to the present translucency that is measured by the Cosmic Microwave Background Radiation when photons were decoupled. Observable evidence from the present universe indicates an accelerating expanding universe and by reverse extrapolation the proposed “beginning” of the universe has been conjectured to have occurred at the time of this proposed “Big Bang”. Certain features of the present universe (Flatness, Isotropy, Isothermal, Adiabatic, Gaussian Density Fluctuations) allow scientific models of the early universe to be created and explored beyond that which can be directly observed. By the extensive and consistent intermeshing and cross matching of the observable webs of evidences, it is felt that a compelling case can be made that a reasonable approximation of the reality of this non observable universe can be made. The best proposed models at the present time are various versions of “Inflationary Universe” where the Universe is proposed to have expanded at a much more rapid rate in the first fractions of a second than the subsequent slow expansion. By presuming that the present models of physics still hold, a time scale is proposed back to this supposed singularity, however this is mere extrapolation of the known physics and mathematical models that we do have at present. The reality is that there is an opaque wall during this “first second” beyond which the mathematical physics no longer works, resulting in this extrapolation being mere unsubstantiated inference. The reality is that we don’t know what happened past a certain point because we don’t have the physics to examine it. The universe may have gone on endlessly, for ever expanding and contracting rather than necessarily having a “beginning”. It may be a multiverse, but we don’t know, particularly as this is beyond the closed causality that allows direct examination. This is only proposed because it is predicted by some of the models that explain many of the observable features of the present and early universe, however we don’t really know. By definition, these proposed multiverses are not open to direct examination so they will remain for ever the speculative predictions of any model that successfully accounts for what can be observed. Religious claims that the “scientific proof of the Big Bang validates the Biblical Genesis” are wrong. Biblical Genesis is religious based philosophy that is unsupported by the present science. Proposals that claim a naturalistic explanation for origins based on quantum fields and vacuum states going into and out of existence are doubtful as they have more of the character of “Something from Something” rather than “Something from Nothing”. “True Nothing” is best considered a philosophical concept. Perhaps true origins is the emanation of the Essential First Cause from an inexplicable absurdity into the Contingent Natural Universe as bounded by the laws of nature (not to be confused with the laws of physics). The laws of nature being, universal, simple, rational (consistent and continuous in time and space), intelligible, closed causal. In our present naturalistic universe, the philosophical questions are, a) is the natural universe, as bounded by these laws, all there is? b) did we discover the law bound natural universe or did we create it as a useful set of boundary conditions to work with? c) if there is more, does the external interact with the natural universe, if so then how and in what way?

        b) Abiogenesis: Still in the stage of scientific conjecture although some reports that a satisfactory naturalistic mechanism is in the offing in the not too distant future. Main ideas centre on various lightning strikes on bubbling pools of chemicals, perhaps sulphurous gases at the bottom of the oceans resulting in the first self replicating molecules, RNA World and Ribozymes. Nobody is saying that these “ideas” are somehow validated, although there is a lot of evidence that is energising research in this area. For now, they are mere proposals in the present scientific bootcamp, so there’s no point anyone claiming that they are somehow “wrong”. Another line of thinking from one particular source, within the undoubted large pool of ideas, is based on the notion of the naturalistic creation of a “gene centred” code in real time. For science to be able to examine this proposal, the mechanism must, by definition, be naturalistic. The neoDarwinian Synthesis of Evolution is a compelling naturalistic explanation for the sequences of the genetic material, DNA, it forms the present consensus. Some scientists believe they can improve on this present consensus, by either replacing or improving on this present consensus with their “gene centred” code ideas. This remains to be seen. Belief that this “gene centred” code is derived from a supernatural agency is pure philosophical belief system and has nothing to do with science.

        c) Consciousness: Surely the holy grail for naturalism is consciousness. Is consciousness an entirely naturalistic phenomenon that is fully open to scientific investigation or is it partly so and partly the most obvious emanation of the supernatural in our universe? Cognition studies, based on concepts in Information Technology and the work of neuroscience, provide a good naturalistic foundation of the way our mind works and the way we think. But we are more than mere zombie like automatrons. Philosophers and religious thinkers have thought about the experiential side of consciousness for hundreds of years. Some would have it that we are on the verge of a naturalistic explanation of the experience of consciousness, others scoff at this idea. The prospect of human designed artificial intelligence is well progressed, but will this provide cognitive zombies or will it be possible to artificially design conscious experience? The prospect is interesting, if not frightening and possibly dangerous.

        No matter what naturalism achieves in the future, the concept of a philosophical supernatural God is under no threat, although the naturalistic claims of supernatural based religions will come under close examination. Is religion the revealed way to know the supernatural source code of existence or is it, itself, a naturalistic phenomenon of our own human nature as we grapple with the existential angst of our own sentience?

        • I somewhat more agree than disagree with you about methodological naturalism. However your statements overlook the fact that theology is the very thing that gave birth to science. There are reasons why. ALL science necessarily has metaphysical and axiomatic underpinnings. I also discuss this in detail in Evolution 2.0.

  9. John Lyster says:

    -Perry I have had a good look around your web site, read articles and some of the blog debates and watched your presentations on videos, but it will take time to look at the books. In the meantime I suppose I do feel I have a pretty good handle on what you are on about.

    -I understand that you have two major projects going on here…………..

    a) Promotion of your own understanding of biological evolution from a designed “self correcting code/principle” DNA molecule as inferred from engineering code. It is your assertion that this model is superior to that of the neoDarwinian consensus based on Natural Selection and Random Mutation which you also assert is now “dead”. I would take this to mean falsified, in proper scientific terminology. You either directly assert (??) or imply that there is some level of “consciousness in the algorithm” that directs the evolutionary process and that was designed into the code by one of five potential designers, most likely God. Your proposal is that this works via a suite of mechanisms which you characterise as “the Swisse Army Knife” or more formally known as “Natural Genetic Engineering”. The implications for potentially reverse engineering this “self correcting code/principle” to normal engineering and information technology are profound.

    i) Looks to me like you have taken from your background as an information and engineering specialist to do a bit of a re interpretation of some mainstream science, that is still generally regarded as operating within the neoDarwinian consensus, when you have relabelled “NGE” as your very own “Swisse Army Knife” based on an analogy from engineering code. Properly understood, the NGE proposal replaces the random mutations of individual base pairs with the entirely naturalistic “higher level” specific environmental stimuli, a sort of physiological biofeedback loop to counter the “dogma of DNA to proteins” that has already been shelved as no longer fully explanatory. Add your theological world view and the analogy from engineering has now been infused with the entirely unscientific “God hypothesis” for designing the code and seemingly sentient DNA chemistry. But your writing leaves me entirely confused about the specifics of your claims in this regard, just where does science end and personal philosophy begin? Scientific rigour is not your forte. You contrast your approach with that of the ID people who claim mathematical analysis of the “non random” DNA sequence infers intelligent agency, which they chose to not nominate, although we all know what they are talking about. Instead of a mathematical analysis of the DNA sequence, you infer similar agency as the source of the code by your analogy (which you call inference) with human designed engineering code. I assert that your proposal is not “Evolution 2.0” but simply, “Intelligent Design 2.0”. The NGE proposal says what it is, NATURAL GE and, as such, forms a legitimate scientific proposal, although I think you and its proponents overcook its status within the present consensus. It seems to me that you have latched onto this because it forms a naturalistic explanation that gets rid of the dreaded RANDOMNESS. Look, I want to be fair here Perry so I’ll be honest. I don’t think that you understand the meaning of this word in science and naturalism. It’s meaning is entirely consistent with an intelligible and law bound universe. I really think you should do yourself a favour and seek out some wise and neutral counsel on this matter. At one point in your videos (where you are speaking, one to one, with another gentleman, Bill Jenkins) you appear to get quite agitated, even angry as you raised your voice when speaking on this topic. Forgive me but I think that you eschew the matter of point mutations whereas NGE looks to include this (??), albeit due to this real time physiological feedback loop rather than randomness and I don’t think that NGE says anything about codes in the DNA. You have quoted strongly from some of those within the NGE “movement” in claiming that their proposal (different though it be from yours…which looks decidedly unnatural to me) is a new hypothesis that replaces the present neoDarwinian consensus. While these people may agree with you on this, to some degree, I would urge that it is going to take a whole lot more than the say so of a few good scientists and your good self to believe that the gigantic edifice of neoDarwinism has been torn down, falsified or is “dead”. If so, then a few Nobel Prizes would be in the offing, starting with James Shapiro and possibly yourself included. Scientific hypotheses must sink or swim by their own recognisance, they do not get falsified (or made “dead”) by other hypotheses. They may be refined by new data or even usurped by a more explanatory hypothesis but not falsified by it (like Einstein Relativity did to Newtonian Classics). The proposed falsification of the neoDarwinian Synthesis is “Rabbit fossils in the PreCambrian”. NGE offers refinement to the neoDarwinian consensus is a more likely characterisation. Within the science, I’m quite sure that you are entirely on your own with your theological implications, self proclaimed “Swiss Army Knife” and seemingly sentient chemistry that has been designed. By any measure, the evidence shows that sentience does not emerge until the level of neurology. All that you are claiming is pure philosophical, indeed religious, assertion. In essence I think that the present neoDarwinian consensus includes all that is canvassed within this NGE (but certainly not your “Swiss Army Knife”) and more and it has progressed a long way from when the synthesis originally came together in the 1930s. Your characterisation of the present consensus as simply random mutation and natural selection is just the basic entry level stuff that is taught at high school biology class 101. I think that your continued mis characterisation of it as such is simply creating a straw man for you to shoot down with things such as your “slot machine” random generator that does more to falsify your own analogy (not inference) with engineering code than falsifying neoDarwinism.

    b) Competition to find a naturalistic explanation for abiogenesis, the “self organising code/principle” as opposed to the “first self replicating molecule” of “primordial soup” fame.

    ii) Looks like a plausible project, look for a natural explanation for code rather than a molecule and leave “design” to the philosophical implications of God. Race is on. The new era of entrepreneurial scientific research. If this project comes up trumps then the commercial returns will be extensive, but possibly more importantly (to some?), Nobel Prizes to follow, especially if “a new law of physics” is found to be behind it all. This last statement might seem to be implausible, however there are some who think that a search for a fully naturalistic explanation for consciousness may involve its discovery as a new, measurable, fundamental property of nature, similar to mass and energy. The search for naturalistic explanations for all observed phenomena should never cease. God loves this.

    iii) My sense is that your naturalistic abiogenesis project is worth while because it is looking for a natural explanation without any teleology. However your new “designed, self correcting code” evolutionary model does not look plausible to me. Perhaps it might transpire that life began with the self organising code, then it self replicated and went on from there with neoDarwinism. Might this first code contain within it the requirement to self replicate and then away she goes? Perhaps I’m just getting fuzzy headed and trying to play nice with this “everybody is a winner” approach. What ever happens, God should remain intact. Perhaps God created/became the laws of nature which deterministically resulted in this inevitable, non accidental, eventuality when the conditions became right. The secrets to unlock are those conditions and the mechanism they resulted in for creating this self organised code/self replicating molecule.

    -Personally, for the purposes of these discussions, I am more interested in how science works to explore the natural world than taking sides about how people might think about the world. That’s not to say that I am not otherwise interested in how other people think and why, including your good self, eg if you don’t mind, your continued use of the phrase “it’s the fact” when making assertions, whereas I’m more inclined to see more shades of grey. Also your web site includes references to having “proved God” on the one hand yet also acknowledging this as not possible on the other. OK, so I note that you explicitly refer to this as “tongue in cheek” on the video but elsewhere such irony is not apparent as there is very emphatic language being used. For me, your continued blending of the religious with naturalism does make it hard to for me to follow if you are speaking specifically about the science, your religious views or simply being confused yourself…..hence my advocacy of the true “scientific mindset” when speaking of scientific matters on this site. eg Regarding your “Design Argument”. In print, you explicitly WRITE your argument as follows; 1) DNA is code, 2) All other codes are designed, 3) Therefor DNA is designed. Very emphatic reasoning by logical deduction, in print. Yet as you speak to this in the video you SAY, “Therefor IT SURE LOOKS LIKE DNA is designed”. Wow, this is just so different. One is apparently emphatic “proof” by logic, the other is nothing more than hopeful assertion.

    -1) On the matter of codes and information I default to your good self.

    -2) Is your inference to design a reasonable proposition?

    a) Logic of the Syllogism and Inference.

    -1. The sequence of base pairs in DNA is a code, 2. All codes that we know the origin of came from a mind, 3. Therefor DNA came from a mind. This is inductive inference and hence inherently unreliable. You have countered that all scientific reasoning is inductive and so to throw out inductive reasoning is to discard almost all scientific knowledge. I would counter that scientific reasoning is an endless cycle of abduction and deduction in order to minimise the “problem of induction” to a high level of certainty as being the “best explanation” at any given time. In science, simple inductive inference is mere assertion, it is only the beginning of the cycle, this is where science begins, it’s not where it ends. I’ll get back to this.

    As I quoted above, you have also more emphatically written……..

    -1. DNA is a code, 2. All codes are designed, 3. Therefor DNA is designed. This is deductive and hence inherently reliable, however this relies on the validity of the premises. In this case, premise 2 is just an assertion and hence this is invalid reasoning. To accept premise 2 is to turn this into an exercise in circular reasoning.

    -I note your syllogism to design and I think it fails as a scientific inference because there is no explanation to test. The hallmark of science is a special type of inference, abduction, inference to the best testable explanation, not pseudo inference by analogy. (Since neo Darwinism does provide a testable natural explanation then it is the present “best” explanation we have, but this can change.) I have written before that inference is only the beginning of the induction/deduction cycle that is the hallmark of the scientific method. For the inference to go anywhere it needs a testable mechanism along with its predictions to compare against the follow up evidence, something that is entirely missing here. Without the testable mechanism the science stops and your inference remains mere assertion in the same way as ID. Indeed, what you have made here is an “argument by analogy” which is a logical fallacy of proof and I’ll explain below why this is actually a false analogy in any case. In this case the inference to design by an intelligence must be by comparing the DNA footprint with the footprint of a known intelligence and the sort of code that it writes. Your “argument by analogy” is false, your discussion is not even inference and without the testable mechanism it is not even wrong.

    b) Analogy. Yours is actually an “argument by analogy” and as such is an informal logical fallacy of proof. In any case it is actually a poor analogy. Just because engineering and biology are similar with respect to code (at least according to your good self) doesn’t mean that they are similar in other respects. Essentially you are comparing apples with pears as you, yourself, emphasise that the information in living systems has “something more” (able to create) than that in engineering systems (just responds to instructions). I fail to see how what applies in the world of engineering code can be so directly inferred (analogised actually) into the living world code let alone inferred to the supernatural world. This is just a variant of what the ID people are doing with their mathematical analysis of the DNA sequence and which you also condemn as poor inference. You write in anthropomorphic language when describing what the genetic code is able to achieve using words such as “know, decide, smart, create, choices”. Are you inferring a certain sentience to the DNA code? If so then surely this simply implies an even greater disparity between genetic code and engineering code and so even further weakens the purported inference link (that is really nothing more than an analogy). It would be better to settle for the reality that chemicals do not contain such “sentience”, this is the emergent quality of neural tissues and their patterns of activity. Surely a non sentient DNA molecule that doesn’t “make choices” is more analogous to the engineering code that “merely follows the instructions of its designer”? At best, your analogy is highly problematic and, in any case, analogy is not logical proof and scientific abduction it is not. So we must move beyond mere analogy if we are going to infer design. How to do this?

    c) Footprint of a known intelligence. Yes, we KNOW that ALL engineering code is (human) designed, we can observe this directly. However this is saying nothing. We need to be able to find a way to assess code of an unknown source and legitimately work out where it comes from, if it was also human designed, without having observed this or having any other knowledge of it. Of course this is a little hard to grasp conceptually because there is a certain self manifestation about knowing that all engineering code is human designed. But for the sake of discussion, let’s just imagine that we came across some code that had us really wondering as to its source, perhaps it was the strangest looking code ever seen and some claimed it to be from an Alien source. If there is any doubt about an engineering code of unknown source then we can measure the footprint of our own intelligence when designing code (what sort of codes we create, the patterns and instructions we make in engineering code) and then compare with the unknown code. This is the sort of thing that palaeontologists and anthropologists do all the time when inferring what sort of society created the residual evidences without direct observation of that society. We know the patterns that indicate how a particular society functioned and if they match the patterns of known intelligence, human beings. eg the tools it used, how they used them, the buildings they lived in, layout of cities, symbolic icons etc etc. In the same way, we don’t need to have direct observation of a human being creating a particular piece of engineering code, we can infer human design by assessing the footprint within the code. Inexplicable, supernatural intelligences, by definition, don’t leave an examinable natural footprint. Something that is completely lost on the ID people who seem to think that they can infer an un-examinable supernatural intelligence from the DNA sequence and just leave it at that. Simple inference is not science, science requires abduction. The ID proposal is nothing but assertion, something I think you’d agree with. What must the professionals who study ancient societies make of all this? We may not know what is the true nature of our own human intelligence, but we do know its natural footprint and the sort of codes that we design and how. The fact is that we leave a measurable, natural footprint that can not be said of a putative supernatural intelligence. Yet you appear to equate the known footprint of human design in engineering code with the unknown footprint of the putative supernatural designer in biological code. Well actually you don’t even appear to be doing that with your inference/analogy what ever, but putting that aside, let’s think about this issue of footprint.

    At best we might be able to look at the footprint of the DNA and infer a human made code by comparing it with the footprint of human made engineering code. Only then could an inference to a testable explanation be made.This is, in principle, possible but no one is doing that. Inference to a testable explanation, this requires a human intelligence that leaves footprints we can see in the code in just the same way as ancient societies left their footprints for the palaeontologists to examine without directly observing that society. In principle a similar inference could apply to Alien made code, but we’d have to know that Alien and the footprint it leaves when designing its code. Another failing of the ID approach when they demur from nominating their so called “inferred designer”. I don’t know if I’m making sense here but I think that you might profit by chatting with some social scientists. Now I sense that you think of human intelligence as supernatural, hence your assertion that “there are no natural designed codes”. Perhaps this gives you the right to claim the analogy (not inference) to DNA code which you also claim is supernaturally designed. However, as I wrote above, you do explain that DNA code can “create” whereas engineering code “merely follows instructions”. Regardless of what is claimed about the intelligence of the designer, the analogy between the codes fail, so we are back to footprint in any case. Perhaps it might be that human intelligence designed the engineering code as “instruction only” and the DNA as “creating”. In this case, the analogy fails but the footprint should be the same. Indeed, it may be a plausible philosophical position to claim that human intelligence is supernatural (because we really don’t have a natural explanation for consciousness…….we just don’t know) but I am speaking of the naturalist evidences (footprint) that emanate from this intelligence, otherwise science can not examine and infer. Anthropologists and Palaeontologists are not concerned with the nature of consciousness. As scientists, they only look for things they can examine, the naturalistic emanations from that consciousness, the footprint. Trying to draw inferences from what we consider to be the nature of human consciousness is futile if we consider it to be supernatural. In any case, this is just baseless assertion from a scientific perspective as we actually don’t know the nature of consciousness, this is simply philosophical conjecture at this time. The only way we can draw any testable inference from consciousness is if we have a perfectly natural explanation for it and I don’t think that is coming soon and I doubt that you’d think this is ever going to be likely. I repeat here, your claim that human consciousness/intelligence is supernatural is baseless assertion from a scientific perspective. For science, we either have a natural explanation or, as is the case here, we don’t know. Some are giving a natural explanation for consciousness serious consideration, I say, “go for it, this is what God wants”. If all of this sounds confusing then believe me I am only at the tip of the iceberg in my own understanding. Suffice to say that it all gets back to footprints in the code from a known intelligence. Perry, you are comparing apples with pears, your inference without explanation fails and your reasoning is simply the logical fallacy of “argument by analogy” and a poor one at that. The bottom line is that we do not know if the DNA has been designed, code or no code. Not unless a human or a known alien did it and we knew it’s footprint. This inference must be drawn from the evidence of a footprint within the DNA code itself, not by your false analogy from the world of engineering. And of course, in science, the inference can only be to an intelligence (leaving aside ideas on whether it is supernatural or natural) with a named and known footprint. This is essentially the failure of ID and its mathematical examination of the DNA sequence, except that theirs is an inference without explanation and yours is a false analogy.

    -3) Where did the DNA come from? Humans, Aliens, Product of Chance, Undiscovered Law of Physics, God?

    -In your discussion of the five proposals to explain the origin of the code, you dismiss 1) Humans and 2) Aliens on account of not ending the infinite regress in favour of 5) God, which does. This is an incorrect requirement in this discussion that lies before us. The purpose of science is to look for such natural explanations without fear or favour of philosophical positions or implications and the question of humans or aliens designing the DNA code is at least an, in principle, scientific project. Going back further into the regress is philosophy. The key to this is looking for the footprint within the DNA code as I discussed above rather than any fallacious inferences or analogies from engineering code. On this basis, human intelligence becomes the best candidate for exploration, leaving Aliens as only an, in principle, candidate until one is found. By definition, God does not provide a measurable footprint so is not a candidate and the other two options (Chance, as you call it, and New Physical Law) are irrelevant to this particular point I am making here. The question of a naturalistic explanation for our (or the alien’s) intelligence/consciousness is another matter for science to consider. In your last blog comment to me, you acknowledge some sort of partial agreement with my “methodological materialism”, otherwise what I call “the scientific mindset of a-THEISM” (not to be confused with the philosophical materialism of Athiesm). I would urge that you are allowing your religious beliefs to enter ‘the lab” and this is causing confusion in your thinking when you use this infinite regress line of reasoning to prefer God to Humans or Aliens. If, per chance, a naturalistic footprint was found in the DNA that pointed to human or alien design then this would be the design inference we are looking for. Looking further into the regress would of course require further investigation from a scientific viewpoint but at least we would be able to cease the enquiry (within reason) with our own DNA. This may sound a bit strange, I am only trying to make the logical point, but of course I am not being practical here. No matter how far back scientific investigation goes into the regress, the issue eventually becomes philosophical or religious, depending on your bent. Claiming “5) God” straight away is simply stopping the science right at first base and that’s never a good thing to do “in the lab”. On the other hand 3) RM+NS and 4) New Law of Physics are much better candidates. However these are not assessed by looking for footprints.

    -4) Problems with your Engineering Code to Biology Code Analogy.

    a) Random code generator. I have elsewhere discussed your random code generator and what I call the “slot machine looking for the golden nugget win”. Now that IS an analogy, I’m NOT saying it is a slot machine, it’s just a comparison for illustrating and clarifying my point. You suggest that the language gets destroyed into unintelligible noise as the mutations proceed and that the chances of obtaining the intelligible “big hit” are so absurdly small as to suggest this falsifies the “random mutations” explanation. In the biological system, there is no need for such “precise language” to be a “successful hit”. The “language of the code” is not a discreet set of intelligible words to a human mind, it is what ever sequence that prescribes what ever it takes for its phenotype to survive. It’s not a specific golden nugget, its anything and everything that either remains or goes away. This is why the maths of population statistics is an entirely different ball game to what you are proposing with your random generator. Population statistics was the third instalment of the neoDarwinian synthesis in the 1930s based on an evolutionary tree that firmly agrees with that of the geographic spread of the fossil record and that of the later molecular chemistry in the 1950s. The way to understand what is going on with the DNA is not with this simple slot machine that is tasked with hoping for the golden nugget code or else unintelligible nonsense builds up as if it is a word in a human language. In the case of neoDarwinism, what “makes sense” stays and “what doesn’t make sense” just goes away, it does not build up. The following quote is just so wrong. “INTERESTING FACTOID: This same process of intelligent evolution is how your immune system learns to fight off germs it’s never seen before: It systematically tries different combinations and once it’s ‘cracked the code’ on the invading disease, it passes those changes onto daughter cells. Your own immune system is a miniature model for evolutionary biology.” The simple maths of your random code generator explain nothing, the sophisticated maths of population statistics explains what is going on here. Perry, you have not explained why random mutations and natural selection is wrong, nor have you falsified this hypothesis. What you have explained is why your “engineering code to biology code” analogy fails.

    b) Noise. You assert that mutations will increase the noise in the code, corroding it and once in can not be removed. Again, this is based on the false analogy between engineering code and biological code. Engineering code mutations WILL create unintelligible noise because this interferes with the decoding of the message to the same sort of intelligence that designed and encoded the original information, us. In biology, the decoded information of the mutated code may very well be “unintelligible” to the code creator (the original environment) but this mutated code now interacts with a new environment, a new “intelligence”, if you will, and if it “makes sense” then it becomes assessed as “non noise” and retained and if it “doesn’t make sense” to the new environment then it is assessed as “noise” and lost. In this way, randomly mutated code is not somehow “corroded”, it is simply changed. It’s the ever changing environmental conditions that decides if the decoded message (as expressed by the phenotype) is to be classed as noise and eliminated or classed as “non noise” and retained. End result is a self culling biofeedback loop that keeps the code clean. Perry, you have not explained why random mutations and natural selection is wrong, nor have you falsified this hypothesis. What you have explained is why your “engineering code to biology code” analogy fails.

    5) Randomness.

    I am disappointed by your discussions on randomness, a mixture of mis understandings, mis representations and straw man arguments to knock down the generally accepted neoDarwinian consensus. You seem to treat the two stages of the neoDarwin consensus, random mutation and natural selection, as being two separate processes to be assessed, and attacked, on their own accounts. I would urge that considering them as two stages of the one process yields a different perspective. NeoDarwinism is partially random, it is not random. Describing this as chance is simply cherry picking a word out of context. Consider also the difference between random and indifference. In the case of the starved and stressed amoeba, the frequency, amount and speed of the mutations changes in accordance with the environment that drives this but the actual individual point mutations are indifferent to the environmental conditions. With this in mind, “random” only applies to a small component of the overall totality that is explained by neoDarwinism, which is itself NOT RANDOM. It’s “goal” then is not into any particular direction or end game but simply to the phenotype that best adapts. You may argue with this interpretation but the difference between the explanatory value of the maths of your random generator and the population statistics is one of the many pointers as to which approach has more success in explaining what is being observed.

    Notions of goal orientation are teleological philosophy, not science. One may possibly philosophise that the First Cause of the Universe created the laws of nature so that conscious sentience would inevitably evolve in a naturalistic, cause and effect, way. I think this is a plausible philosophical position to adopt, but it’s not science. Of course this carries with it the implication of determinism. Now if one thinks that our intelligence/consciousness/minds are purely naturalistic then we are bound to lose the sense of self and free will. OK, so that’s a problem for Theology, but my philosophical God of First Cause, the inexplicable Absurdity, is unfazed by such assertions. But none of this is science. Moving right along, you comment that the primordial soup hypothesis of abiogenesis is a random accident that goes against science. I would counter that this is not so. Once the certain set of conditions prevailed, abiogenesis became statistically certain, it is simply our task to find out what those conditions are. Lottery analogy. The lottery will eventually be won with statistical certainty, but we don’t know where and we don’t know when. Again, one could possibly propose that the Prime Mover had in mind those set of conditions as an inevitable certainty once he set up the laws of nature and its endless deterministic cause and effect. In this way, abiogenesis is not a random accident but an inevitable consequence of the grand designer. The job of science is not to wonder about such philosophies, the job of science is to propose natural mechanisms and test them without fear or favour of philosophical positions or implications. In watching your videos I can see an obvious emotional reaction against this word, so much so that you won’t even accept that science is doing what it does best when it makes a proposal such as “primordial coup”. Conjecture, proposals and testing in the bootcamp stage of science. Of course the primordial soup hypothesis is still in the conjecture stage, but the way you speak of it indicates to me that you consider it stillborn before a specific explanation has been tested. It appears that you’d prefer that science dismissed this without a proper examination, I consider this to be an emotional bias. I think that the better attitude to adopt is to allow all proposals that are in-principle possible, ie naturalistic, to remain on the table and then “may the best man win”. In this case it is “first self replicating molecule” vs “self organised code”. The only proposals that science should dismiss are those that have no, in-principle, chance of being examined, supernaturalism.

    You rail against the concept of randomness as if it is a lawless godless phenomenon that has no place in god’s universe or in science. This is an incorrect value judgement placed onto a mis representation. I would urge that you consider the concept of stochasticism as it applies to the statistical mechanics of thermodynamics and quantum mechanics for example. What may look random and chaotic at one level is actually law bound at the level of probability statistics. Otherwise we would have no science of thermodynamics and statistical mechanics, indeed any statistical analysis at all. We may not be able to examine the “random” behaviour of individual atoms in the microstates of a gas but the certainties of the Gaussian probability curves assures us that we can be sure about the rule bound behaviour of the macro states of PV=nRT. Indeed, it’s possible that, in a law bound Universe of deterministic cause and effect, we can make an in principle assessment of the movements of individual gaseous molecules that fully eliminates what we perceive as randomness (because it is not in reality), however the maths of this is too great and the need is too small, hence the use of statistical mechanics to assess macro states is based on the law bound universe. In the law bound universe, the movements of the gaseous molecules in the micro state only APPEAR to be random, it’s just that we don’t have the maths to solve for this. The behaviour of sub atomic particles does appear to be random at an individual level, but ultimately they are governed by lawful probability distributions. The point mutations of base pairs is individually random, but they can also be statistically analysed because they are governed by probability laws. Perhaps, just like the gaseous molecules, there is a deterministic cause and effect about these point mutations that we are unable to measure with our present science and hence they only appear to be random. Randomness really is a word that needs a lot of thinking about and I only have a sense of it myself. However, my understanding is that it is not the simple “Godless” characterisation that you have given it. I would urge you to have a re appraisal of your understanding of randomness in this law bound universe. Indeed, the only true capriciousness that I am aware of in this Universe is that of the religiously proposed supernatural agency that intervenes in our natural world. I’m not opposing this concept, but it’s just not science. Quotes: “That it happened randomly, spontaneously and accidently is non scientific”. No, this is not understanding the science of randomness. “The answer is the belief that the universe is structured, orderly and the equations are beautiful”. Yes, this is why the population statistics of evolution works, just like the statistical mechanics of thermodynamics. “The next layer is not more random chance and chaos, the next layer is even more orderly than the one we know”. Yes, this is stochastics, the organising principle is stochastic. What appears to be random at one level is law bound at the next level. This could never have been without the law bound Universe. I’ve recently spoken with a pretty dry scientist who does not have a faith orientation and he has expressed wonder at the seemingly inexplicable “organising principle” behind the apparently certain probabilities of stochastics. The simplest explanation is that this is simply an emanation of our law bound Universe, but is this an explanation or mere observation that has something else behind it? Is the Universe quintessentially law bound or is this a human construct of a sub section of reality that we wall off in order to make sense of it? Now we are definitely “out of the lab”.

    -5) Consilience and Consensus

    Consilience is an important concept in understanding the science of neoDarwinism and why the edifice of its consensus its not about to crumble in an instance (non contextual quotes from the young and brash Stephen J Gould aside). This concept is important in understanding just how strong the consensus of neoDarwinism is and how it overcomes the anomalies in the evidence base that inevitably exist. It means that there is broad based agreement between different and unrelated methodologies that all point in the same direction, in particular the overlaying of their predicted evolutionary trees. The consensus is not based on endless amounts of the same evidence, but on the way different methodologies predict and match the same pattern of the evolutionary tree. The predicted trees of Mendelian genetics and molecular chemistry cross match like the palms of an open hand on top of each other and with what is found in the fossil record, yet they all come from different and independent methodologies. Significantly the predictions of the population statistics (that so differ from your slot machine analogy) also match up into the overall synthesis and evolutionary tree. Of course there are issues and anomalies, but the broad consensus is that this all holds together, the Synthesis. Competing naturalistic explanations for the tree of life must match and do better than this consilience in order to overtake it. They must be simpler, more broadly explanatory and above all, naturalistic. Think of this level of evidence as being like the lawyer who must convince the court of “guilt beyond reasonable doubt”. It is not enough to present endless amounts of the same evidence, he must convince the court with different types of evidence that allow examination of the case with different methodologies that all lead to the same conclusion. In this way then, endless samples of the same blood stains will not do it. What is also needed are witness statements, alibis, motivation of the alleged, weapons etc etc and all led to the same inference. No single evidence base does it. Science is also built on consensus. For some issues, such as the simple cause and effect of Newtonian Mechanics, the consensus was easily reached and soon passed beyond much doubt (problem of induction aside). Falsifying this would be easy as one anomalous data point on the charts would be enough to falsify this. This is science 101. For big picture items such as the neoDarwinian Synthesis the consensus was much harder to achieve and required the sort of concepts that you don’t learn about in science 101, eg consilience and statistical analysis of vast data sets that are simply lost on the general public. The modern issue of climate change is another case, the consensus is still evolving but the broad understanding appears to be getting there. It takes such a lot of data, that must be cross matched into a consilience, that for these “big science” issues, consensus will be much harder to obtain. On the other hand, unlike simple Newtonian mechanics, it is much harder to falsify. You don’t just find a few anomalies and claim “it’s dead” or “this discredits the whole theory” as I have seen with discussions about the “Global Warming Hiatus” and Anthropogenic Climate Change (AGW). They say that the way to falsify modern evolutionary theory would be “Rabbit fossils in the Precambrian”. Well if one was to be found, this would not actually falsify the consensus in the Newtonian Mechanics sort of way, it would just make us think in a Bayesian sense about more likely probable reasons, such as some local fault line in the layers. For surely, if a legitimately falsifying rabbit fossil were to be found in a non contextual layer, then it would be but one of many such fossils found. It takes a lot to build up the consensus of “Big Science”, it takes a lot to falsify it. So who “runs” the consensus? That’s a hard thing to nail. For stuff that’s ‘locked in” (as much as anything in science is), then the consensus is in the texts books. For climate change, well this is kinda’ hard, it seems to be a certain evolving zeitgeist at the moment, but the best place I think to look are the position statements of the various science academies, although certain political forces prefer to “bash the science” and have us eschew these statements on account of “the scientific establishment”. For neoDarwinism, I think the broad brush has now percolated into the school texts books and some of the “drill down” issues are still making their way into the post graduate material. As the consensus firms up, it will move it’s way down to the school books. I’m no expert on NGE, however it is my understanding that the facts of its processes are well within the vanguard of the science, however its all about the interpretation of the explanation of these processes. Whether they contribute to and upgrade the present consensus or eventually become a new consensus, only time will tell, but I think we are a long way from seeing the neoDarwinian consensus overturned.

    -6) Anthropomorphising the Natural World

    The tendency to anthropomorphise the natural world is a natural human tendency, we see spooks in the dark, we create humanoid myths about the natural environment. While this may be understandable, it doesn’t help create a good scientific mindset in the lab. Teleology may be interesting philosophy, important theology, but it is bad science.

    Your discussion of how your “code centred” evolution works seems to me to littered with anthropomorphic sentiments. Cells know, the code decides, cells are smart, wilful genome, creative code, “we must know the intelligence of our opponents”,”biological systems make choices”, what do cells know that we don’t?”. Indeed, all of your discussions on the Natural Genetic Engineering appears to indicate some sort of conscious sentience going on at the level of the chemistry of the DNA molecule. This, I would urge, is a total mis representation of what is going on at this level. More likely, we simply have James Shapiro like physiological, chemical biofeedback loops, similar to the way Natural Selection acts as a non chemical biofeedback loop on the mutations. By any measure of what we know in natural science, sentience only begins to arise at the level of neurology and electrical circuitry. Even then the lower levels are only unconscious reflex loops, leaving sentience only at the very highest level of sophistication and complexity. Of course you are entitled to propose anthropomorphic like agency in the natural world, but not “in the lab”.

    -7) Fine Tuned Universe vs Anthropic Principle.

    -“There is no law that says there has to use a four letter alphabet (A/C/G/T). It could just as well use a 6 letter alphabet or a 2 letter alphabet (1/0). Thus DNA gives every indication of having been designed.” My understanding is that a four letter code is the most efficient system, yes. Of course the religious mindset claims “fine tuning” whereas the non religious will assert “anthropic principle”, the reason we have a four letter code is because it is the most efficient and this is how it has evolved because nature works like that. This is just the tip of the iceberg of this “anthropic” vs “fine tuned” conundrum that is simply about world view and, in my view, is the very reason why God is a philosophical concept that can not be “proved” or “disproved” by science or logic, as I see poor old William Lane Craig trying to do. These double edged arguments (one argument used either way or two opposing arguments which have equal plausibility) will form the basis of entertaining debates and of course will be traps for the naïve, but they are essentially futile arguments either way. There is so much of this in these “God debates”. I consider this goes to the core of what is my philosophical inexplicable Absurdity, nominally identified as “God” and anthropomorphically characterised by our religions. Another example of these two edged arguments that comes to mind is the “fine tuning” of the Cosmological Constant. God did it or the fact that our universe is the way it is makes this value an inevitable certainty. Depends on whether we are looking backwards from our present state or forwards from Origins and God. I think of a “lottery analogy”. The chances of winning the lottery are infinitely small. If the religious inspired person wins it then he will claim agency, especially if he prayed before the results came in. The non religious person who runs the lottery will claim statistical certainty, inevitably someone wins it. The chances of the win are 100%, God has nothing to do with it. It all depends on one’s perspective and world view as to what one makes of it. Whether we are the winner and looking out, or the lottery agency and looking in. When you write what you have written above I am inclined to respond, “well so what if it is 4?” In another universe, if a 6 code system was more efficient then naturally it would end up being the code system in that universe. No matter what value we observe in the universe it is going to be what is required to be the universe we observe, otherwise it would be a different universe. Perhaps in another universe, consciousness could well have evolved in a cockroach and we would think female cockroaches were beautiful creatures. I’m sure you are fully aware of all this and have your objections and the blood pressure is elevating. Personally I’m not pushing any particular barrow on these debates, certainly not in the lab. I’m just stating that none of these arguments carry any particular weight in proof or disproof of God, except in the theatre of debate winning strategies. God is above winning debates or naturalistic proofs. All one has is plausible philosophy or religious faith. Science doesn’t do God, but it does have a lot to say about the naturalistic claims of religion.

  10. John Lyster says:

    -8) Quotes

    “The fact that an intelligent being designed the Toyota car is actually the first thing you need to know.” This applies to engineering design however, for the reasons discussed above, it is fallacious to infer this into putative biological design of DNA. If you assert that the intelligence of the “Toyota designer” is supernatural then this is not science, it is philosophy. The only way that science can examine the human intelligence of the “Toyota designer” is by way of its evidential footprint, not by claiming “I saw this guy in the Toyota lab and he was beavering away on his design software therefor I know it was a human that done it”. Knowing the footprint of an unknown code allows us to infer its designer, not because we have first hand observation of its design and creation. This is what is required to infer design and, in principle, is what will allow us to infer design in the DNA. But only if we can recognise the footprint, hence human design is the only possibility. While one may regard human consciousness as philosophically supernatural, the task of science is to find natural world footprints of how it designs, infer mechanisms and then make predictions on what evidence we might see of further human/engineering design.

    “Intelligent code has more information in it than the laws of physics”. This seems to me to be unsubstantiated assertion and if it is so then I’m not sure how one can then go looking for the self organsing principle that purportedly has more information in it than the laws that allow us to look for it. I’m just confused by this statement.

    “Recognizing the work of a designer is not any more anti-scientific when we’re studying DNA than when we’re studying Toyota Corollas. It just acknowledges that there are some things that are not reducible to mere physical laws.” Physical laws are the stuff of the natural sciences, perhaps we need some help from the social sciences. Again, we “recognise the work of a designer” by examining its footprint, not by fallacious inferences and analogies that don’t work. Toyota designers have a naturalistic footprint in their code that supernatural designers do not have. The best one can do is to look for human designed footprint in the DNA code that is similar to that in engineering code. If such footprint were to be found in the DNA then we might be able to infer human design…….at least in principle.

    “Case in point, you cannot reduce the rules of any computer program to mere physical laws. They obey physical laws 100% but they also follow additional rules set by the programmer. To pretend there’s no programmer is not just unscientific, it’s foolish. It actually prevents you from ever fully understanding the program.” The rules that a computer programmer sets up in the computer code are an example of the footprint of a human designer. Proper science doesn’t go into the computer lab and look for an actual designer to observe and then claim, “oh, there I can see him working away” therefor it was designed. For this we would literally have to see the designer for every engineering code ever designed before we could be sure of its source. There has to be something else that allows us to infer design without having observed the designer. This is footprint. Proper science looks for footprints in the code to see if it can predict the unknown source of other code. We have to have a naturalistic way of inferring design without having had direct observations of the designer, this is how the Anthropologists work as they don’t get to make direct observations of the human intelligences of ancient societies. All of this is irrespective of our beliefs regarding the nature of our own consciousness. However, the putative supernatural designer has no footprint, by definition. Perhaps some discussions with some social scientists might be in order, beats me.

    -“Therefore living things are better studied in the same manner that we study car engines than in the manner that we study apples falling out of trees.” a nice allegory of how you think vs atheist. However I would urge that your reasoning is wrong. You are undoubtedly comparing the “living things” of DNA with the consciousness of the car designer when going on to make your (failed) design inference. If we are to make the inference of design in the DNA then we need to have a measurable and testable quality of the car designer’s consciousness that we can then go and look for in the DNA. In this way then, both the car engineer and the falling apple are the same, for they both require naturalistic qualities that can be measured and then factored into an inferred explanation of their respective phenomena that can be tested by predictions. Of course no one is suggesting that a falling apple is a designer, I am merely writing about how they are examined as naturalistic phenomena and in this way they are the same. So putting aside the question of just what exactly human consciousness is, the naturalistic quality that allows us to infer design is through the way the designer reveals the way it works, its footprint. The only designer that we have a footprint of is the human designer and no one is looking for that in the DNA code. I have only a basic grasp of all this so may I suggest some consultations with social scientists, philosophers and neuro-scientists in your area. The fact is that we don’t know what the nature of human consciousness is although some people are working on this (and when they do this in the lab then they must adopt the scientific mindset of “methodological materialism”, whether this conflicts with their philosophical or religious beliefs or not). However we can observe and measure its footprint. In this way then, I feel that the car designer’s footprint and the falling apple are the same, the first is a social science the second is a natural science.

    -“Science cannot operate apart from philosophy and draws very significantly from theology. Science need not be pitted against philosophy or religion, and science cannot be practiced in a vacuum. It’s OK for scientists to admit that the origin of life question takes us outside the boundaries of science.” The job of scientists is to continue looking for naturalistic explanations, irrespective of personal beliefs and not to presume anything about the “origin of life” that is actually pure philosophy. I don’t think that scientists must “admit that the origin of life takes us outside the boundaries of science” at all. Such a question simply should not be on their radar when they are “in the lab”. Suggesting scientists should “admit” to your personal philosophy is just bullying in my book. For the scientist working “in the lab”, it’s a case of having a naturalistic explanation or “I don’t know”. Even if a fully acceptable naturalistic explanation for abiogenesis is found (yes, just as in your own abiogenesis project) then the scientist “in the lab” will not be thinking about what goes on “outside the boundaries of science”, by definition. By now your blood pressure is probably rising as you wonder why I’m being so picky and pedantic, but I think that what you write here goes to the issue of your bringing God into the lab as is clear in so much of your commentaries. On the matter of “outside the boundaries of science” the scientist does not have to admit anything, he simply has to be tabula rasa. As soon as he steps “outside the lab” and is no longer a scientist, then he can “admit” to what ever he believes and that may not be what you believe. For me, the philosophical “answer” to the origin of life may well just be when the Prime Mover created the law bound naturalistic universe. But I don’t really know. The “scientific mindset” really does not draw any implications from putative Gods but I can see that it has an impact on your religious convictions. I consider that science and scholastic Christianity share a “common ancestor” with the European philosophical traditions rather than a linear progression. Yes Christianity appears to have contributed to the cultural milieu that allowed the studies of the law bound Universe to flourish as opposed to the pure mysticism of other cultures. I do acknowledge the biblical references to the intelligible universe that I would think were a part of the flourishing philosophical culture, but I am not sure this can be claimed as validation for the supernatural claims of religion. But I’m just a foot soldier in this game. I appreciate your perspective on this non scientific issue even though I seriously challenge your perspective on the scientific issue here.

    -The primordial soup event should happen more than once if it was an accident”. Given the right conditions it probably did, in the same way as “Apes to Humans” appears to have happened multiple times. It is statistically impossible for “Apes to Humans” to occur because of one single event and in the same way this probably explains abiogenesis. This kind of thing requires sophisticated statistical analysis which is beyond my scope, however I do appreciate that this is the thinking. Of course this is all conjecture, in particular in relation to abiogenesis. When you write this do you have in mind the prospect of multiple parallel life forms simply existing side by side on planet earth? Surely this is not sophisticated thinking?

    -“How to get from soup to code?” (self replicating molecule?) “It’s pure speculation, a non explanation”. Exactly, there is no explanation at the moment. Dismissing scientific conjecture as a “non explanation”, as if this ends the issue, is just shooting down the strawman of conjecture before anyone is making any claims.

    -“DNA has a conscious intentional designer” This is an untestable philosophical assertion. Of course if your competition is successful then this will negate this claim.

    -“Does life harness undiscovered laws of physics? Are there unknown emergent properties in nature?” Well these must all be naturalistic if it comes under the purview of science. I’ve read where some people are considering the possibility of finding a way to quantify and measure human consciousness as a fundamental property of the natural world, in the same way as “energy” and “mass”. Then it would be possible to examine consciousness using the mathematics of physics and even create laws of consciousness. I doubt that this is what you had in mind here, but if there is an “undiscovered law of physics” then a Nobel Prize will be in the offing. Are there “unknown emergent properties in nature”? I bet we are just barely scratching the surface on this one but consciousness is considered to be an emergent property of the way our neurology works. I do not agree with some of the language you use when writing about the DNA code. One would think that you imply a certain sentience at the level of DNA chemistry and I have discussed this elsewhere.

    -“Cells re-engineer themselves, in real time, in hours… even minutes. The reason you have to finish your antibiotics is, germs can hyper-mutate at terrifying speed – then kill you with a vengeance.” I would urge caution on this point. You are no doubt writing of “real time” changes within the cells where as “hyper-mutations” that explain antibiotic resistance usually refer to inter generational changes. Please please, I doubt that bacterial cells “kill you with vengeance”. You may be annoyed that this is just being “pedantic on semantic” however I would contend that, given the overall sense of your writings, there is a little bit more going on here and that this comes from a tendency to anthropomorphise ALL the natural world. To some degree I can see why someone with a religious background might do this however I just think one needs to be very circumspect about the tendency to do so when writing within a scientific contect. Nevertheless, it is clear that the animal kingdom does share layers of human like qualities and who knows what might be the case in the plant kingdom and, at what level, do certain “human” qualities emanate in the living world? But bacterial cells and vengeance? Of course I would argue against the religious project to anthropomorphise the supernatural, but this is simply a matter of personal philosophy and world view. It is certainly not a matter of science…..BY DEFINITION. It’s going to take a whole lot of scientific studies on consciousness before we can begin to even think of bacterial cells as somehow “little human beings” in this way. Your call. I am not trying to annoy you here but instead offer a genuine prompt towards the truly scientific mindset when you are “in the lab” (regardless of your personal faith orientation “outside of the lab”). I’m actually trying to assist with some gentle (??) pushback here and would hope that you see it that way.

    -I found your discussion on the prospect of finding a new law of physics to explain the self organising code, at the 29 minute mark of “The Video”, to be particularly perplexing. “All codes that we know of (engineering) are designed by an intelligence therefor DNA code was also designed by an intelligence and since DNA was intelligently designed then it was not naturally designed as nothing we know of was not intelligently designed, therefor there is no use looking for a law of physics” said at a rapid and confusing rapid pace that sounded all “sciency”. I think you are saying that such a law of physics would entail the existence of a naturally designed code but no one has ever seen this, so dna code can not have been naturally designed, so therfor there is no use looking for a new law of physics. Something like that. I played and replayed this a number of times and it just became more confusing to me. We do not know what is the nature of human consciousness. You claim that it is not natural, this is just baseless assertion. Outside the lab, philosophy and belief systems are what ever, but inside the lab we either have naturalistic explanations or we proudly proclaim that we don’t know and so keep looking without fear or favour of philosophical implications. By saying that we don’t know what consciousness is (no natural explanation) would have helped to avoid the trap of false analogy and invalid inference. It would then have encouraged us to look for a measurable naturalistic quality in the engineering code that could have been used to test for design inference in the DNA code. The human design footprint. Your commentary here, and I took the time to really have a good look at it, just looks to me like a confused case of argument by false analogy, passed off as inference which is not even testable, circular reasoning and baseless assertions that are designed to get to the answers that you are looking for (no use looking for a new law in physics, we are heading towards God). Sorry for being so hard on you.

    “Your will to discover the truth has to be greater than your fear of what ever that truth might be”, a nice way to finish Perry, however this is philosophy. Science deals in best and latest natural explanations, truth is not on the scientist’s radar.

    -9) General Comments.

    -Your use of Kalam beginning and Leibnitz explanation style arguments is plausible philosophy however you riddle it with with emphatic language, this seems to be your way. I think of natural explanations as compelling or not and philosophical positions as plausible or not. Shades of grey.

    -You appear to have backed off God from direct intervention and tinkering in evolution to the code designer in order to work out how you think that evolution works. I guess I have backed off God further into the infinite regress where the inexplicable Absurdity created or became the of laws of nature (not the laws of physics). I feel that this philosophical position better assists me to adopt scientific mindset when considering matters “in the lab”. It seems coherent to me.

    -Laws or rules of nature. That the Universe is intelligible, simple, law bound, rational and consistent (in time and space), universal, closed causal.

    -You make much of how the neo-Darwinian consensus is dead, based upon the energetic claims of a young Stephen J Gould and the work of a few scientists who, while they may be doing excellent work, have a long way to go before the edifice of the consensus is torn down. The concepts that are described in the “Natural Genetic Engineering” appear to me to be a part of the recognised mainstream science although I am not qualified to make a clear assessment of the context. They are in the post graduate text books, they are mainstream, but of course with a difference inference to explain them than yours or James Shapiro. Such is the nature of how science works.There are a couple of excellent publications by one Bruce Alberts.

    https://www.bookdepository.com/Molecular-Biology-Cell-Bruce-Alberts/9780815344643?redirected=true&gclid=EAIaIQobChMI_6yPw9nU2AIVGQQqCh1oagByEAAYASAAEgJF1_D_BwE this is a very sophisticated tome at the post grad level

    https://www.bookdepository.com/Essential-Cell-Biology-Bruce-Alberts-Dennis-Bray-Karen-Hopkin-Alexander-D-Johnson-Julian-Lewis-Martin-Raff-Keith-Roberts-Peter-Walter/9780815344551?ref=pd_detail_1_sims_b_p2p_1 a counterpart at the undergraduate level that is more readable

    https://vimeo.com/192682257 I think that Ch 6 of this book looks to be the important one.

    -Scientific hypotheses sink or swim on their own recognisance, they are not falsified by competing hypothesis that share the race for the most broadly explanatory and simple explanation. At this stage it seems to me that these so called “Natural Genetic Engineering” mechanisms will or are already updating the present consensus. In the above books, the proteins that do all this snipping and cutting have been prescribed by the DNA that has been naturally selected. OK you have a different inference about what is going on, perhaps you need to enter the peer review and contribute to the scientific consensus. This is how science works, this is how the consensus changes.

    -Much is made of all this being the world’s best kept secret or ignored, lashings of conspiracy abound. From what I can see these mechanisms are all fully part of the mainstream science, albeit with a different inference. How much and where they get taught is of course up to its degree of acceptance and the level of course work. Perhaps it is not appropriate to be going into such layers at high school level and unless the consensus is locked in then not much at the undergraduate levels either. The inference may not be to your liking but this looks to be the present consensus and, no question, it is the stuff of mainstream post graduate science. There is no “evolution industry”, there is “nothing that they are not telling us about” or “not putting in the text books”. https://www.ibiology.org/genetics-and-gene-regulation/transposable-elements/#part-1

    -I found your “why” vs “how” questions discussion to be very confusing, particularly the discussion in relation to the curvature of blood cells. To me this was infused with the presumption that a supernatural agency is behind the design and also that this purpose is designed. If this is the thinking in the lab then I can see that naturalistic mechanisms will become harder to find because of the loss of the “scientific mindset”. Science asks “how” questions without fear or favour, why questions either don’t have an answer or are merely a prompt for someone to express their world view. This really does have many implications into how one approaches the scientific method that I can not go into here, but if you don’t mind my saying so, and you probably do, then I see evidence of this all over this web site. Teleology has no place in the lab, outside then all bets are off.

    -Labelling the neoDarwinian synthesis as being about accidents and randomness and then claiming this is not science is just creating a straw man argument and shooting this mis characterisation down. See above discussion on randomness.

    -I am confused at how the originally designed code self edits with this “Swisse Army Knife” of mechanisms but then maintains the quality of this design feature, post edit. It’s all very well suggesting that the original code was designed by an external agency, but this is very different to all of the post edit codes. Or are you suggesting that there is some sort of “spookey know factor” that is unrelated to the sequence within the DNA but allows it to retain its original design quality, regardless of how it has been self edited? This is getting very spurious to me.

    -Your discussion of the nano cell with 500,000 base pairs and the unlikelihood of getting golden nugget style king hits in the vast array of possible combinations is just another mis representation of the true reality of how evolution works. Evolution is not picking locks, looking for pre defined block buster code combinations, it is just creating random codes that either work (adapt) or don’t. This conceptual basis creates an entirely different type of statistical analysis, the population statistics of the neoDarwinian Synthesis, compared to your simple slot machine analogy.

    -I have previously mentioned that Gödel’s Incompleteness Theorem provides an interesting basis for your discussion of the external God of Christianity, however I expressed mild reservation over its logical applicability as a proof. This was just an initial hunch. Well it didn’t take me too long to search the net and come to an answer on this question. Essentially the Gödel’s Incompleteness Theorem applies only to axiomatic formal deductive systems (e.g. mathematics). Theology is not a formal system, it is inductive. You may say that this theorem is an analogy that you use to explain your philosophical world view, however you can not claim a mathematical proof as having any formal relevance to a supernatural being. I used to think that the Heisenberg Uncertainty Principle “proved” my philosophical position that the world is inherently uncertain. Well, that was when I was in high school. Making these sorts of extrapolations is just “jumping the shark”. I watched your video discussions on the Gödel Theorem with an open mind and in particular the assertions about the Trinitarian Nature of God. Quite honestly I just got lost in all the confused blather. In order to maintain some level of decorum here, I just think it’s a case of “the less said the better” here.

    -“And what about consciousness? In the human realm, only conscious beings create and modify code. Where does consciousness come from? Are cells self aware?” Well greater minds than mine are looking into what constitutes and defines consciousness and HENCE where and at what level of biological complexity it rises. I would urge caution on the conflation of unconscious chemical/physiological biofeedback loops with basic low level reflexes, with animal awareness with full blown human sentience. If you don’t mind my suggesting, I feel that your commentary here gets decidedly close to Deepak Chopra style confusion by the religious way that you seem to interpret this “organism-genome-organism” feedback loop idea, being that you seem to imply some level of conscious effort on the part of these cells. From my perspective, this layering of neural activity from the most basic reflex to the most highly developed cognition indicates the evolution of consciousness rather than the sudden appearance of any such “soul” or what ever. The one thing I am absolutely sure of (to the degree of “fact” dare I say) is that this issue of consciousness has been barely touched on from a naturalistic perspective and still has so far to go. At the cognition level, there is certainly a lot of naturalistic understanding of consciousness and as an information technology person I’m sure you have a good handle on this. The experiential side of consciousness, the sense of the self, is the big conundrum. There’s a lot of philosophy and religious belief about all this of course, but from a scientific and naturalistic perspective, we just don’t know. I do share your interest and excitement, but I am very, very much “jury still out”. I just have a sense of your religious convictions entering into your analysis of the science here.

    -“How do we end up with symbolic/semantic information from a bunch of chemicals?” Conjectural challenge for you if I may please. Just a thought experiment for you as I am certainly not qualified to challenge you on the topics of information and code. May I suggest that there is no quintessential information in the DNA sequence or genetic code just as there is none in a book that is not read. The sequence of the letters in some written material is a representation that has meaning (hence information) to the source code (the writer) and then to the end user (the reader). If the reader can not decode it (read that language) then there is no information. Information exists in the minds of the writer and reader, which are of course both naturalistic intelligences (in cognition, not experience). In the same way, the information in the DNA sequence is not quintessential, it only has “meaning” in that it mediates the source code message (environment) and is then interpreted in the end user (phenotype) that adapts. ie, if you simply had a strand of DNA molecule in space with no environment and no phenotype for it to mediate, then it would indeed be simply a bunch of chemicals. The information in the DNA is only “meaningful” when it exists between the earthly environment and the adapting phenotype. In the same way, perhaps we should be careful not to inject meaning onto something that is otherwise inert, such as the letters of a language, when that meaning really only exists in the minds of the writer and the reader. You asked “how do we get symbolic information in the first place, how do we get semantic information if we are only starting with chemicals?” Your approach is very much about looking at the genetic code as having the quintessential symbolism in it, then the possible inference that some sort of supernatural agency is responsible for having inserted it vs the naturalistic mechanism that you are looking for in your competition. May I propose that the “information/symbolism/semantics” lies within the coder and encoder, the environment and the phenotype or the brains of the author and reader of a book, while the chemicals of the code (letters in a book) are simply bits of inert chemical that carry no quintessential meaning/semantics in themselves. Just a thought bubble.

    -A place for religion. Perry, for me “God” is a philosophical concept, the inexplicable Absurdity at the end of the infinite regress, the Leibnitz Essential Explanation of the Contingent Natural Universe. It might even be the Kalam Beginning of the Natural Universe, however our present physics doesn’t allow us to be too sure on that one and I doubt that will ever change. This concept seems to give me congruency when I think through science but for you it is possibly not far off the dreaded atheism. For me, religion is a naturalistic world, psychological-socio-politico-cultural phenomenon that allows societies to “self boundary” and individuals to handle the existential angst of this absurd universe. The more religion is about the psychology of the individual then the more I accept it, the more it progresses into socio and culture then I get more wary of it. When it gets political then it is dangerous. ie, it works best as a personal belief system and engages community for those who need it or dip into and out of it as desired. But its involvement at the larger levels has been the problem that is the lesson from so much of history. To me, attempts to anthropomorphise “God” are understandable yet they seem to me to clutter thinking about how our Natural Universe works and doing good science. I could just as easily enter a Church building for the naturalistic benefits of emotional comfort it can provide, I can feel relaxed about those who seek its community and socio-cultural benefits, but I get frustrated at its politics. Outside the lab I am really not fussed, except for religio-politics. However it seems to me that the project of Theology works in reverse to the other two project of Philosophy and its famous offshoot, Science which progress forward from the tabula rasa to where ever the reason, logic and evidence leads. To me, Theology begins with its answer and spends the rest of its energies reverse justifying and rationalising its pre ordained answer. Perhaps this is OK as a belief system, but I think it does not help the “scientific mindset”.

    -So I understand that there are four main historical arguments for God. 1) Moral; I consider that we have the “God given” nous to work out how to get along in our lives and that, in effect, principles such as “do no harm” effectively inspire our laws now. But that’s just scratching the surface. For me it’s values and ethics. 2) Ontological; I understand that this is no longer accepted as carrying much weight (??). 3) Teleological; acceptable philosophy but please don’t bring it into the lab. 4) Cosmological; for me, the Leibnitz Argument about the Essential First Cause that explains the Contingent Natural World is a plausible philosophy.

    -Finally, everyone in the lab should be an a-THEIST. When you are outside the lab you MAY be an Atheist (but it doesn’t matter). A definite belief in supernatural agency may interfere with one’s thinking if one carries it into the lab, just as much as definitive Atheism can interfere with one’s philosophical outlook outside of the lab. I believe that the acceptance of a plausible philosophical God is congruent with my understanding of science. However I don’t share this view about some aspects of the naturalistic phenomenon of religion. Richard Dawkins comes across as the “strident Atheist” whose aim is to the bring about end to the “God Delusion”. In my mind, he is perfectly entitled to do this, if this is his philosophical belief. However, I think he can only plausibly have issues with religion and not with God. Putting that aside, I am always disappointed that he can come across as the unofficial spokesperson of science and so, in this way, give science a bad wrap when he attacks religion and God. Stephen Weinberg says “Scientists don’t think enough about God to know whether they are atheists or not”. I think that Richard Dawkins possibly carries his excellent “scientific mindset” too much “out of the lab”. On the other hand, I am astounded by what I see, hear and read coming from seemingly highly qualified and intelligent scientists and professional, such as these Creationists, the ID people and your good self. I think the problems arise because you all carry your, understandable, religious philosophical teleology too much “into the lab”. Teleology puts purpose and design ahead of cause, it starts with God. In the lab, the best thing one can say when starting out is, “I don’t know”. The scientific mindset truly begins with the blank slate. If naturalism is part of “God’s plan” then this is best left to philosophy “outside the lab”.


    -I’ve been very hard hitting at times, I hope you don’t mind. I think you are up for it. I bet I get it wrong in many places. I’m just a foot soldier.

    -mine is a philosophical God along the lines of the Leibnitz Argument from Cosmological Contingency. I can not, in all honesty, ascribe it any particular characteristics except that it forms the philosophically plausible explanation for the Natural Universe. For me, it is an inexplicable Absurdity. Yours is a religious God with, what appears to me, to be anthropomorphic characteristics. Teleology is important.

    -I am perplexed at the interpretations of natural history by often highly qualified people from a scientific background, in particular the Creationists, ID and even your good self. What is going on here? May I suggest a lot of psychology and socio-culture, but I am particularly interested in this issue from an epistemological point of view. Am I missing something?

    -Two words appear to stand out as being a problem for you. NATURAL selection and RANDOM mutations. What ever one thinks about the consensus of the neoDarwinian Theory and whether it deserves its present status as the best explanation, it IS natural. Science asks for nothing more. Random is a very sophisticated concept that is not quite what it seems, as I’ve just touched on above. It is very much a part of the law bound Universe that is philosophically ascribed to God. May I propose that thinking of this as the one process with two stages rather than two independent processes would help, well this works for me anyway. In this way, there is a certain indifferent, if not statistical, quality to one component of an otherwise non random process. Random is not random and chaos is not chaos, both are law bound in a probabilistic way, both are statistical.

    -Science doesn’t do God but it may have something to say about the naturalistic claims of religion. Science either has a compelling “best” naturalistic explanation or it doesn’t know.

    -Differentiate the methodological materialism that is the scientific hallmark “in the lab” from the philosophical materialism of some, “outside the lab”.

    -Leave Teleology “outside of the lab” and try to develop the scientific mindset that begins from the tabula rasa when “inside the lab”. “Outside the lab”, all bets are off.

  11. John Lyster says:

    Hello Perry, I found this article in “The Guardian” and thought I’d give it a critique if you might be at all interested. Quotes are indented (with quotation marks) and my replies are below each.


    -“Complex biological systems have not been explained by neo-Darwinian processes”

    A baseless assertion that goes against the overwhelming consensus and consilience of the present neoDarwinian Synthesis. In any case, even if this statement were true then it doesn’t validate the ID proposal. Each hypothesis must provide its own positive argument that proves to be more simple and broadly explanatory than a competing hypothesis. Attempts to knock down competing hypotheses with negative arguments does nothing to validate ID. neoDarwinism provides a positive testable argument, ID does not. Check the position statements put out by all the reputable scientific agencies. I don’t consider one particular meeting put on by the Royal Society in order to explore “New Trends in Biological Evolution” as impacting greatly on that consensus. “New Trends…” says it all, it is not “New Consensus in Biological Evolution”. Scientific meetings are all about looking at naturalistically based proposals, all inputs are gratefully received and will, if considered valid by the peer review, contribute to the vast and overwhelming present consensus in time. The Shapiro proposal looks to be interesting, it is naturalistic, but it is unlikely to bring down the edifice of neoDarwinism in one fell swoop. But who am I to say, I am just a foot soldier in the suburbs who follows the consensus? Perry, while your proposal takes on board the NGE mechanisms it is clear that it doesn’t carry the same naturalistic inference (abduction). Scientific consensus evolves gradually, it doesn’t pendulum swing from hypothesis to proposal and back again. Of course there will be gaps and anomalies in the evidence base of any vast consensus.

    -“The plans, you report, come “in the wake of a recent survey commissioned by the British Council which found that 54% of Britons agreed … that ‘evolutionary theories should be taught in science lessons in schools together with other possible perspectives, such as intelligent design and creationism’.” As a former science teacher and schools inspector, I am disturbed that proposals for science education are based on near-complete ignorance of intelligent design. I also think the views of most British people in this matter should not be so readily set aside.”

    Science is not a democracy. It is based on finding the best explanation by natural mechanisms, not the views of the vox pop.

    -“It is an all too common error to confuse intelligent design with religious belief. While creationism draws its conclusions primarily from religious sources, intelligent design argues from observations of the natural world.”

    Not so fast. Observations are only the starting point. Inference is not enough. Science requires a testable mechanism, abduction, inferred from the observations and then the consensus gradually builds or falls away as this is compared with further evidence, in a never ending cycle of further inference (abduction) and deduction. Observations are just the start of it.

    -“And it has a good pedigree. A universe intelligible by design principles was the conclusion of many of the great pioneers of modern science.”

    The philosophy behind science (Theology for some) is that the Universe is intelligible by being Rules and Law Based. Apart from Human Design with its observable footprint, “Design” is a philosophical/religious proposition. Naturalism can not look for the putative supernatural design as it does not provide a footprint we can measure.

    -“It is easily overlooked that the origin of life, the integrated complexity of biological systems and the vast information content of DNA have not been adequately explained by purely materialistic or neo-Darwinian processes. Indeed it is hard to see how they ever will.”

    The consensus of neoDarwinism is built up by the vast evidence base, its consilience, its simplicity, its broadly explanatory success and above all its “pure materialism”. This is what it means to be naturalistic. I sense unnecessary teleology coming into this chap’s idea of science. If it is to be criticised for being “purely materialistic” then I can see how this is why there is a problem going on here. Science, BY DEFINITION, looks for “purely materialistic” explanations. This is not a criticism of neoDarwinism, this is EXACTLY what it does. Inferences to “something beyond” materialism MUST mean an implication of the supernatural, surely? This is philosophy.

    -“In an area such as this, where we cannot observe what happened directly, a legitimate scientific approach is to make an inference to the best explanation. In the case of the huge bank of functional information embedded in biological systems, the best explanation – based on the observation everywhere else that such information only arises from intelligence – is that it too has an intelligent source.”

    Lashings of your false analogy and non inference between human made code/information and biological code/information. I’ve discussed elsewhere the way to assess the source of code is the footprint of the DNA and how it compares with that in human made code. This particular statement is a terrible mis characterisation of abduction. “Inference to the best explanation” does not mean a supernatural intelligence. Supernatural intelligence is NOT an explanation in the scientific sense, though it may be in a philosophical sense. What is required here by “explanations” is a natural mechanism. This is just saying “God dunnit”.

    -“You quote schools minister Diana Johnson, who says: “Learning about evolution is an important part of science education.” If so, then thinking about what must have preceded it is also a legitimate area for science. The school pupil’s question is always going to be: where did it all come from?”

    In which case the school pupil is sent to social studies or comparative religious studies class. This schools minister needs to go back to school. Specifically, we don’t have a naturalistic explanation of “what must have preceded evolution”. This is why people like yourself are looking at abiogenesis. When science doesn’t know, it says so and then butts out.

    -“There is a tendency in school science to present the evidence for evolution as uniformly convincing and all-encompassing, failing to distinguish between what is directly observable – such as change and adaptation over time through natural selection – and the more hypothetical elements, like the descent of all living things from a common ancestor. The evidence for these various strands is not of equal strength.”

    Science is about the BEST explanation that we have, regardless of what is claimed about the different evidences. The “best” is all we can hope for, if people pass it off as “uniformly convincing and all encompassing” then that’s just a mis characterisation. Inevitably, being the “best” that we have also means that it will have holes and deficiencies which is why science is about continuous refinement of the “permanently provisional”.

    -“If you insist that intelligent causation is to be excluded in the study of origins then you are teaching materialist philosophy, not science.”

    Science is about METHODOLICAL MATERIALSM, it is not about philosophy. “Intelligent (supernatural) causation” is just teleological assertion and has no place in science.

    -“I believe current government guidance is wrong in denying intelligent design the status of science.”

    From what I’ve read of your writings, I think we can both agree how wrong this statement about ID is.

    • I do not agree with the ID movement such as it has been put forth by the Discovery Institute and others. There are many fine distinctions to be made and most of your questions here are answered in Evolution 2.0. You need to read the Appendices as well, especially “All About Randomness.”

  12. John Lyster says:

    Question to Perry, do you have any follow up comments on what I’ve written above please? jl

  13. John Lyster says:

    Hello Perry. Do you have any follow up comments on what I’ve written above please. All the best jl

  14. John Lyster says:

    Hello Perry, I’ve read this page on what appears to be your own term “Telorexia, blind to purpose in nature” and its discussion on randomness (when I did a google search for Telorexia it just came up with your commentaries in the results, or commentaries about your discussions) and this “yet PZ seems unable to see that error correction is by definition purposeful! “. I think this goes to the core of your interpretation of science, TELEOLOGY IS SCIENCE. Then quotes such as this, “PZ responds by further describing those systems that correct errors, yet PZ seems unable to see that error correction is by definition purposeful!” and ” is a process that follows active logical patterns; and that cells re-engineer their own DNA in response to shocks and threats.” and from Barbara McClintock “cells are smart and they re-arrange their DNA in very specific ways when faced with common threats, and very clever ways when presented with unique challenges.” and “Cells detect when things go wrong and set them right. You can’t avoid purpose in nature, or teleology.” and “Personally I suspect cells may possess some level of self-awareness. McClintock even asked, “What does the cell know about itself?” and “No matter how purposeful a cell is, it can’t fix all of them”. Throughout all of this is language infused with presumed anthropomorphising the natural world, either by way of implication or by direct statements. Or is the reader to take all of these comments (including your quotes of McClintock) as some sort of allegory, which is very hard to differentiate in context as you slip slide your way between implication, direct assertion and this vague allegory. Please state what you mean and mean what you say. Perhaps the “best” of this lot is “Personally I suspect cells may possess some level of self-awareness.” Here is your core position, completely baseless comment but I grant you that you demur with “Personally I suspect…”. So I will take this as just “musings on the side” rather than science. Perry I just get totally lost in all the obscurantism. However, the main point I wish to make goes back to your heading. In a previous post I state that the problem in so much of your discussion (and of like mindeds) is this matter of bringing Teleology into science, yet here you wear it like a badge of honour in your title. What exactly do you mean by “purpose”? If this is a naturalistic purpose as in “the purpose of evolution is for the genes to pass on to the next generation” then this is science because it is talking about testable natural explanations but playing lose with the language. However, it is clear that you have in mind something more, the notion of what our intelligences make of “purpose”. Of course, in psychology and neuroscience, this is an in-principle examinable notion IF it applies to a naturalistic intelligence. However if it implies a supernatural intelligence then this is untestable. Hence it is not science, not because science is somehow “anti supernatural” but because it can not examine such a thing….this is philosophical conjecture. Yet your use of the terms “design” and “purpose” just confounds me as your effortlessly switch between what appears to be natural and supernatural “purpose”. One might argue that the “designer” of the DNA sequence is natural selection. Equivocating language is such a no no in science……say what you mean and mean what you say please.

    • John Lyster says:

      “Randomness simply means “no pattern.” So when any complex system exhibits behavior you don’t understand, then you as a scientist have no right to declare it’s “random.” Because as soon as you do so, the scientific method itself – which is the search for patterns – stops. ” The term used is “indifference”. There ARE patterns in the overall trends of the mutations and this can vary due to local factors within the cells, however INDIVIDUAL mutations are INDIFFERENT to these factors. Think stochastically. The proposal that these INDIVIDUAL base pair mutations are random is not based on “system exhibits behavior you don’t understand”. The behaviour (individual base pair mutations) can be assessed as such because the mathematics of population statistics, which is based on such mutations, beautifully describes and predicts the evolutionary trees as described by the evidence of the fossil records and molecular chemistry. It is certainly not predicted or described by your “slot machine” random generator model that seeks to discredit neoDarwinism but instead merely discredits your false analogy.

  15. INDIVIDUAL says:

    Perry, you rail so much against “Godless randomness” as if this is what neoDarwinism is all about, indeed it is but one small aspect of one component of a two stage mechanism. Properly understood, it merely refers to the INDIFFERENCE of individual base pair mutations within an overall statistically analysable process whereby the overall trends of mutations shows higher level patterns. In addition is the “guidance” (careful of the equivocation here) from natural selection to weed out the noise and so called corruptions. Weed out equals SELECTION, as in natural selection. The fact that this can be analysed by the studies of population statistics shows just how Laws and Rules bound this all is. NeoDarwinism has, as one of its vital pillars, the consilience of the fossil record, the molecular chemistry and how their evidences, the evolutionary tree, all match up to validate this law and rules based statistical analysis that is partly based on the indifference of the INDIVIDUAL base pair mutations. Their really isn’t much randomness going on here, if it was then there would be no population statistics. Slot machine generators looking for lottery style hits is just an awful straw man argument.

  16. John Lyster says:

    OK Perry. I can only hope that you have appreciated that I have closely studied your web site, videos and written material and that I have applied myself in earnest to providing legitimate challenges to your thinking. I hope you can even get a sense of another perspective and that I have given a lot of thought to this. Otherwise good luck with your competition and book sales.

  17. John Lyster says:

    Last comment then. Bye bye Perry.

    PS. Listening to the audio of Perry Marshall vs PZ Myers.

    Unlike Information Technology, “Random copying errors would inevitably lead to constant IMPROVEMENT in time”. From the neoDarwinist “perspective” there is no such thing as these value judgements, things don’t get better or worse, good or bad, fit or unfit, it is simply about adaptation….for better or worse….the post mutation sequences that remain are not in any way an “improvement”, they are simply the ones that result in adaptation to the changing environment. They have a more adaptive “FIT” to the changing environment, they do not represent the layperson’s meaning of “fitness”. Perry, you may not agree that neoDarwinism is the best/only/in any way an explanation for the evolutionary changes that have been observed. You may think you have a better proposal based on “purposeness”, good luck with this and hopefully we’ll see you present to the peer review. However, in the meantime, I think it behoves of us to not mis represent alternative and competing theories in our discussions.

    In the discussion I note that PZ also refers to zerbra fish “improving” and “getting better” in the lab environment, but as he also informs us this is “better, as used by evolutionary biologists” in that they “better at living in the lab but less able to live in the wild”. Fitness is relative, depending on the environment.

    This is not about secular/humanist/atheism vs religion……..each to their own. This is about how science works, what it does, what it claims, what it can claim. Teleology (be it a human inferred sentiment or perhaps even an actual supernatural reality…….take your pick) and anthropomorphising the natural world have no place “in the lab”.

  18. John Lyster says:

    Hello Perry, I notice that you have deleted the last two comments so no matter what I write here will be quickly deleted I’m sure. Perhaps that gives me an opportunity and permission to write some observations of your style that you won’t exactly like but that’s the way it goes. Of course I could go the serious ad hominen but then that’s not my style, indeed pointless any way. You expressed an overall approach to seek “the truth” without fear or favour, fine sentiments indeed. Nevertheless it is clear to me that you have your mind set on your own special “pet hypothesis”, come what may. You have so much personal skin in this game now that nothing’s going to change this, not now or in the long run as far as I can tell. It seems to me that, at the heart of all this, is your attempt to reconcile your faith orientation with your acknowledgement of the science and observations of evolution, something the Catholic Church seems capable of achieving without resorting to marketing their own fake believe science project. Not to mention your preposterous expectation that you have got it all figured out in your own head and have embarked on what looks more like a massive marketing exercise to promote your “wonderful” pet theory than a genuine search for understanding and an explanation. If you were genuine then you would present your proposals to the peer review instead of following in the footsteps of the equally preposterous ID crowd and “jumping the queue” by making direct appeals to the naïve general public and so bypassing the peer review. I have taken the time to give all the stuff on your web site a fair going over and made what I feel are genuine challenges to your commentaries in a fair and civilised manner, but you have simply dismissed all that I have written except for one momentary and most begrudging acknowledgement that you “more agree than disagree with methodological materialism”. How very magnanimous of you? Instead I have received endless plugs for your book as if reading that is going to bring me up to greater speed than all the other research I have done on your web site and even listening to your debate with PZ Myers. I referred you to the wonderful text book on the biology of life forms by the esteemed biologist, Bruce Alberts, President of the National Academy of Sciences, wonderful tomes that are the very distillation of the totality of the vast enterprise that is the scientific consensus, a publication that is one of many put out by the NAS that is regularly updated as new understandings are achieved by the “permanently provisional” scientific consensus. But not a comment from your good self in reply, just more plugs for your lightweight self published non theory in the parallel universe. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002743

    Instead you prefer to waffle on in exaggerated tones about being in the company of mavericks and outsiders such as Bill Gates, even comparing yourself with those other outsiders McClintock and Shapiro. I’m not sure they would return the compliment. Perhaps you are on the vanguard of some sort of Khunsian paradigm shift that will further devastate the already mortified neoDarwinian consensus. Perhaps it is the neoDarwinists who should consider themselves as the outsiders since you, yourself, have pronounced this vast consensus as already dead on the non contextualised say so of a single young and overly excited scientist, Stephen J Gould way back in 1982. What a preposterous claim, such over the top hubris, but it’s clear that this is your style. Perry, as a scientist, you appear to make an excellent IT entrepreneur. Please stick with your daytime job.

    • I have un-deleted four of your comments (all of them redundant) and re-posted them. I did not delete anything else.

      You do not understand information theory, or information entropy, or genetics, or bioinformatics, or evolution.

      I indicated that I will not engage with you until you have read Evolution 2.0 from cover to cover, including all of the appendices. I suggest looking up references as well. If you have any questions about this, please re-read http://www.evo2.org/ny2018.

  19. John Lyster says:

    hmmm, late night postings in Chicago town Perry? You must be related to Donald of twitterverse fame. I’m actually pleased that you have left them up in the end, not sure why you deleted them in the first place as they were relatively benign compared to some of my other comments. Oh sorry, they were “redundant”. Phew, I just read my last comments to you….oh dear, please excuse me. You assert “You do not understand information theory, or information entropy, or genetics, or bioinformatics, or evolution.” Yes I have no background in engineering, IT, bioinformatics (??) but I have a tertiary qualifications in the life sciences and feel I am very much up to speed on entropy, genetics and evolution (at the Undergraduate level). To be honest my main interest is in the philosophical grounding and epistemology of science, what it knows and investigates, what it can claim to know and investigate and I have sincerely attempted to tease out the deficiencies in your thinking and understanding but of course “keeping it all above the belt” so to speak. The book by Bruce Alberts et al is a significant educational resource in your country and it devotes a chapter (ch 6?) on the very mechanisms that you have re interpreted as being somehow ignored by the scientific mainstream. Of course you are entitled to your own interpretation of what is going on, which also seems to me to be at variance to what James Shapiro interprets. Perhaps I should demand that you read this book from cover to cover before I engage with your comments but that would be demanding way too much. It took my engineering/physics PhD brother two years to get half way through it. He has a background that looks to be similar to yours except that when he decided to look into the biological sciences and the PRESENT evolutionary consensus, he could look no further than these two books. Yes I am pleased that I could be of assistance regarding your NY 2018 resolution. Lastly, I wish to quote myself from elsewhere on this blog, https://evo2.org/purpose-desire-review/#comment-45908 “This is ALL ABOUT DEFENDING THE QUALITIES OF SCIENCE THAT HAS LEAD TO ITS “UNBELEIVABLE” SUCCESSES. It has nothing to do with the various philosophical beliefs and assertions that occurs “outside the lab”. “In here” we need more rigour for the success of science to continue, “out there” it’s any body’s business what they believe in. With no operational definition and no testable explanatory power, Teleology just has no place “in the lab”.” I really couldn’t have put it better myself.

    • John Lyster says:

      1) I have had a read through your “For/Against” page and it is pretty nice although I don’t think I share your politics. Such is life in a democracy. 2) OK I accept that you have bigger fish to fry than flogging off a book for royalties. That was just a bit of a light hearted dig. However I do feel that you come across as merely telling people about your position, what people here call “broadcasting”, rather than engaging others on their perspectives. You have a story to tell but it’s not a two way street so it seems. Of course this is your site and you can do things your way and, yes, I can accept that you’ve had to deal with a lot of inane time wasters and haters over the years. Believe me, I really do feel I have a good handle on your work, I am not just yelling at you or trying to needlessly shout you down on this tiresome “religion vs atheism” nonsense. I HAVE made the effort to seek out your position and to challenge you in a civilised and INFORMED manner that is OUTSIDE and irrespective of the “faith divide” but based on “how a scientist thinks”. I have not said that I will not read your book and other book recommendations as this will take time (but I have checked out most of these sources and authors on the net) and so for now I made the effort to make a serious assessment of the information on your website. I feel I have a pretty good handle on what you are on about. Here’s what I wrote in a previous post, “Yes Perry, I won’t believe you or your book.” This is not just saying I won’t ever read your book but, admittedly, I am not in a hurry. I just prefer to read REAL science (phew lol) and to look at non science only in so far as it gives me a brief handle on how “the other half thinks”. That might come across as prejudicial and dismissive, arrogant even, but unless what you wrote in your book is decidedly different from what you are on about on this website and unless you intend to present your proposals to the peer review, then I feel justified in stating this. I’m not inclined to think that endless tit for tat exchanges over the minutia of details and personal interpretations (personal, when it should be before the peer review) is ever going to get very far as essentially I think this is about our views and expectations of what science is and what we think we can get from it. I am more interested in a general understanding of what we can expect from science in a very general, indeed philosophical sense, since this is where science comes from (not withstanding your belief that it evolved from Christianity. My take is that this is more by way of common philosophical ancestry than linear evolution, if you get my drift). It’s why I think that if you believe that you have a serious scientific proposal to make (instead of a boastful self acclamation of a personal pet hypothesis) then you need to do what all the other scientists out there must do. Present to the peer review and contribute to the consensus. I’d actually love to know what James Shapiro might make of your efforts. 3) I do not have a Richard Dawkins style desire to bring about the end of religion as we know it, except when I get angry at religious violence, but of course this is just a short term emotional reaction. However religious inspired politics, including US Style, also angers me. Yes yes, the “league ladder” method of “validating” one’s personal belief or unbelief system by toting up the history of death and destruction and then announcing the winner as the mob who had a lower death count…. please leave me out of it, zzzzzzz. In any case, this is all other matters of socio-cultural-politics, I’m more interested in epistemology and the foundations of knowledge. I have given a fair bit of thought about why seemingly intelligent and highly trained people who, should know better, get their thinking so awry, well in my humble opinion anyway. Of course the extremes of this are the highly educated scientists and lawyers of creationism and especially that ID mob. Religiously inclined scientists who otherwise accept the way science works but suddenly have a problem when it comes to science that SEEMINGLY embarrasses their faith, but doesn’t have to unless one has an obsessive compulsion to a literal translation of the bible. Actually that’s the easy bit and can be easily understood as some sort of psychological issue. However, I will give the ID people more benefit of the doubt, actually I think it is a matter of giving science more credit than it deserves. Philosophical Materialists like Richard Dawkins believe that naturalism is all there is and, in this way, believe that science can, and will, tell us ALL there is. When he walks out of his lab he keeps his “Methodological Materialist” hat on, he is entitled to do that, no one can deny his sincerely held philosophical position……..please don’t drag science “out of the lab”……..same advice I would give to religious people, but in reverse. When in the lab, “please don’t bring God in here”. God is, by definition, supernatural, science doesn’t do supernatural, therefor science doesn’t do God. Otherwise, people are entitled to infer (not abduct) their own philosophical implications from the findings of science. But INFERENCE IS NOT SCIENCE….SCIENCE REQUIRES ABDUCTION. Most people appear to have a rather benign acceptance of the scientific project and acknowledge its processes and conclusions at reasonable face value until or unless it impacts upon emotional hot buttons or vested interests, such as with the climate change issue or even health issues and “alternative medicine,” what ever that is supposed to be. Then it’s often conspiracy theories and amazing mavericks vs “the scientific establishment”. You have done your level best to work through this and, given your faith orientation, it can’t be easy for you and I respect that. However, I just think you are allowing your faith orientation to overcome your science training (and it’s philosophical basis) and reacting a little too much to Richard Dawkins’ “strong Philosophical Materialism”. To me, what is important is to go all the way back to the way science developed out of NATURAL PHILSOSOPHY in Europe, something that the Catholic Church observed first hand and has developed a more sophisticated understanding of than the US style, more biblically focused, evangelical religions. What is the purpose of science, what does it do, what can it claim to do? Can science tell us everything, as the ID crowd appear to think, or does science simply have a job to do and from which we might draw our own philosophical inferences? When physicist David Mermin suggested that the Copenhagen interpretation of Neils Bhor re Quantum Mechanics was best described as “Shut up and calculate”, he was succinctly describing the scientific dilemma. Are we getting a clear description of the nature of reality or just a useful tool that works? Of course Einstein thought that we could get to a better understanding of “reality” and was sure that important hidden variables were being missed. Alas, it seems that he was wrong, perhaps this allegorical God of the unknown does play dice, it seems that this “God” does “hold his cards” in probabilities and uncertainties (dare I say it, randomness). But even this is only about the natural universe, no one here is talking about a putative supernatural being. No matter which side of the debate, when in the lab, these chaps didn’t have the supernatural on their collective radars.

      So what comes first, a personal philosophy that science must validate (please excuse me but your commentaries absolutely reek of this) or to search for NATURALISTIC explanations of observed natural phenomena, without fear or favour, because they work? Is this about finding ways to justify or “prove” our philosophical positions, a definitive reality, what ever that is, or simply about best explanations? One can see the history of Western Philosophy and the two streams of thought on discovering the nature of reality. The internal ideas and ideals of Plato through to European rationalism of Descartes et al vs the external practicalities of Aristotle through to the English Empiricism. Distilling the combination of these evolved into the scientific method and its examination of the natural world. But there seemed to be a Faustian pact, in order for this project to be so successful, it had to wall off it’s deliberations to natural explanations. The supernatural was left behind for the philosophies and pure rationalism of our ideas and ideals. Is naturalism all there is, did we discover this, or did our philosophers find a way to make sense of the absurdity by partitioning off the natural from the supernatural? Did we discover naturalism or did we invent it? Is the rule and law bound Universe, open as it is to our examination, God’s creation, or simply a self emanation? Opening up science to the supernatural is about destroying its utility and that’s a far too successful thing to mess with. Science is about explanations that can be tested, hence abduction and not mere inference or analogy. For explanations to be testable (make predictions) they simply must be natural. Teleology of human design and purpose is based on testable explanations, psychologists and cognitive scientists do this all the time. Unless we are looking for evidence of human teleology in DNA code then we can not find a testable, naturalistic explanation of the code. We can not know the ways of a supernatural “mind”, BY DEFINITION, as we can not test its mechanisms. In science, inference and analogy to the supernatural from the natural world is not enough. Science requires abduction, inference TO THE BEST EXPLANATION (“best” as in “the very best we can provide at any given time” as per the consensus of the scholarly and expert peer review). Science requires positive arguments for its claims that succeed on their own account, inference by appeals to negative arguments about the gaps in other “best explanations” are logical fallacies. For science to work, as best as it can, it is materialist. Philosophies about a background supernatural entity, it’s characteristics, its presence within our natural world are not science. No arguments from you here I’m sure, stating the “bleeding obvious” as the Englishmen would say. However you do exactly the same as the ID mob, except they INFER supernatural design from the DNA sequence and you INFER it by your analogy with IT code. Where’s the positive argument, the testable mechanism, the abduction?

  20. John Lyster says:

    Uh oh, I suspect another delete episode. Perry, if you are serious about your proposal and publication, why don’t you contact NIH boss, and fellow Christian traveller, Francis Collins, and get him to read and appraise your book? I wonder what your “committee member” Michael Ruse makes of it? In any case, true science is about publishing to the peer review, it is not about the vox pop of a web blog shout fest, including yours truly. I notice that you refer to your mechanisms as “Cellular Genetic Engineering” as opposed to James Shapiro’s “Natural Genetic Engineering”. You have taken your cues from James Shapiro but while his is a genuine scientific (as in Naturalistic) proposal, it is clear that yours is not. I’m not trying to be a curmudgeon here, but it looks like you have taken a shining to his ideas as he claims non random mutations, however this looks like where you part company. It would be interesting to know what he makes of your proposal and “inference to design”. Lastly, I’d like to propose a consideration to explain how I think science works, what it claims and what it can claim. Suppose a person prays to the Almighty for a lucky result in a lottery. He does this ten times and wins ten times in succession. The religious, indeed anyone, would be inclined to believe his prayers had surely been answered, direct supernatural intercession had occurred. The inference to design would be hard to deny and at a philosophical level, one may suggest there is something going on. This is up to the individual interpretation and can neither be supported nor denied. But what does science make of this? Science requires more than mere inference, it requires abduction. Science needs to infer a best explanation for linking the prayers to the lottery wins. Even a hundred wins in succession following prayers and none when prayers were not offered would still not be science without abduction of a testable mechanism, even if the inference to supernatural intelligence gets stronger with each win. Without abducing a mechanism we have no way to predict what comes next, no way to test it and further refine the explanation as further evidence comes in.

    • ALL scientific theories are based on inference. No exceptions. The fact that you do not know this, and yet at the same time, you won’t even read a book, is why I don’t engage with you.

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