Skeptic Jerry Coyne trashes “Evolution 2.0” – without even reading it first!

330px-Jerry_Coyne_at_The_Amazing_Meeting_2013Jerry Coyne, Biology Professor at the University of Chicago, reviewed my new book Evolution 2.0: Breaking the Deadlock Between Darwin and Design. He begins his review by saying:

Although I haven’t read it….”

Then he gives his critique of the description of the book… rather than the book itself!

I believe in fair debate. Though I disagree with many of Coyne’s conclusions in his book Why Evolution is True, I actually recommend it in my “Recommended Books” appendix. (And yes, I did read it.)

Coyne’s salvo starts with:

“He does have a degree in engineering, though, as we know, even if we consider engineers “scientists,” their profession harbors a disturbing number of anti-evolutionists.”

True dat. The “Salem Hypothesis” observes that engineers, computer programmers, medical doctors and dentists consistently doubt old-school Darwinian evolution. Why?

Because engineers know how hard we work to design products and write code. Doctors know the smarts it takes to diagnose and treat disease. In our actual life experience, “Random Mutation and Natural Selection” is never sufficient to solve any problem. We know how incredibly subtle design decisions are. They involve elaborate trade-offs. We know machines and computer programs, oddly, never get better when something breaks.

One of reasons I wrote this book was to show precisely those kinds of people that evolution is still, in fact, true! Because evolution is reproducible in the lab – it’s not just a historical theory. The experiments are absolutely fascinating.

My #1 audience is precisely practical, get-it-done, engineering type people. People who don’t find “Natural Selection” to be an adequate explanation for dizzyingly sophisticated machines and systems we see in biology.

Natural Selection is not enough. And what I discovered was 70 years of abundant research that shows cells actively re-structure their DNA, adapting to threats in real time.

Whenever I describe these experiments to engineers, programmers, doctors etc., they suddenly become fascinated with evolution – even if they were hostile to it before. Even ordinary folks at dinner parties lean forward when I start telling them the untold evolution story.

So I am very much pro-evolution. But Jerry Coyne does not like my version of “pro evolution.” Why? Let’s go to some of his criticisms.

When I say:

“Nearly every cell in your body can edit its own DNA, negating random destructive copying errors, charting a path for its transformation (page 82)”

Coyne says:

“Yes, that can happen, for cells have an exquisitely evolved mechanism to edit flaws in DNA (that mechanism, of course, got here via natural selection, since those individuals that could correct the largely deleterious errors in DNA would have more fit offspring).”

Pay attention here: He just told you that natural selection explains it, since the cells with error correction survived and the others died. [Notice he side-stepped answering the question of where the error correction came from in the first place. Zero explanation.]

Also notice Coyne gets the cause and effect exactly backward. How does selection create anything?

And where did that fabulous DNA error correction come from? That’s a FASCINATING question. An important question. It deserves an answer. But “natural selection” is no answer! It is a non-answer.

When I say:

“Genes – far from being set in stone – actually change and adapt to the environment.”

You’ll notice that once again, Coyne just reverts to “natural selection” as though this somehow explains anything.

Everyone knows natural selection is nothing more than eliminating the losers. It’s death. Selection makes room for the winners. It makes LOTS of room for the winners, by the way. A 1% advantage can become a 100X population difference.

But natural selection by definition doesn’t create anything at all.

And so it goes, all through Coyne’s critique.

Q: Genes change and adapt to the environment. How?

Coyne’s answer seems to be: ‘Never mind those exquisite signaling systems or regulatory systems. Never mind how bacteria alter their own DNA, depending on which role they’re assigned to play in their bacterial colony. Never mind the hundreds of signals they monitor from their environment.

‘It’s all just natural selection.’

Coyne: “But if by this Marshall means that genes can adapt to the environment in real time, changing in a way that’s both inherited and permanent, then he’s wrong.”

Barbara McClintock won the Nobel Prize for proving that her corn plants did exactly this. Her DNA changes were in real time, they were inherited, and permanent. James Shapiro confirmed bacteria do the same thing. These are indisputable facts.

Why does Coyne not want you to know this???

About Barbara McClintock, he literally says, “Move along, folks; nothing to see here.”

My friend, that is why I wrote this book. Because the real evolution story has been largely untold. Oxford Professor Denis Noble says every pillar of the classical Darwinian synthesis has been overturned. Meanwhile, Coyne’s version of evolution is dead. 70 years obsolete.

There is LOTS to see here. Do not move on. You could even say McClintock made a greater contribution to practical evolutionary science than Charles Darwin himself. Why? Because McClintock showed where evolutionary variation actually comes from!

Before her, nobody knew.

Coyne doesn’t want to talk about Barbara. Her experiments in 1944 disproved the model he’s still clinging to now.

Chapters 11-16 of Evolution 2.0 explore five major topics that Coyne’s famous book, and nearly all popular “evolution books” say little or nothing about: Transposition, Horizontal Gene Transfer, Epigenetics, Symbiogenesis, Hybridization, and the linguistics of DNA. All of these are spectacular, non-random, real-time systems of cellular engineering.

Without these, natural selection would have nothing novel to act upon. No conversation about evolution is complete without these tools of Systems Biology.

Evolution flows from the cell’s ability to cut, splice, edit, re-arrange and re-program its own DNA. Which is pretty trippy when you stop to consider about what is actually going on. The cell is built from instructions in its DNA… yet it has the ability to alter those very instructions.

Wow.

We barely understand how this works. We only know that it works, and it works very well, thank you very much.

Again, dear reader… why does Coyne say “Move along folks; nothing to see here”?

I repeatedly find this smug, dismissive, anti-science attitude all over atheist literature. “Aw, there’s nothing all that impressive about that. We already knew that a long time ago. Barely worth mentioning. Hey everybody, let’s raise a toast to Natural Selection!”

Do you see how anti-discovery and anti-research this is?

I ask: How do cells generate new information and genes that did not exist before?

Coyne: Yes, that occurs by either natural selection itself, [Recall: Natural selection kills. It doesn’t create. Everyone knows this] gene duplication followed by natural selection, [yes, gene duplication does create new coding sequences, that is my point] or the adoption of genes from other species by “horizontal transmission.” [which once again is a point of the book. Glad we agree on that, Mr. Coyne.]

So notice here that Coyne is actually confirming what I say in the book, while appearing to disagree. He’s reluctant to discuss any of the details of how all this works. It’s all just… natural selection.

Suppose you asked me, “How did Starbucks take over the world with stores in malls, city squares, airports and hotels?”

If my answer was “Pressure from thick competition” and “Most of their rivals simply went out of business” … and then every time you asked me about their strategic store locations, their capital raising strategy, their quality control systems, or their management philosophy… if I just kept changing the subject and chanting, “Survival of the fittest”…

…Wouldn’t you start to feel like I was dodging the question? Or maybe I didn’t really know all that much about business?

Suppose you asked your sports fanatic friend, “How did the New England Patriots manage to beat the Seahawks by 4 points in the Super Bowl?”

What if he just kept saying, “Playoffs, playoffs, playoffs”?

What if you asked him about the stats, the referee calls and the defensive strategy, and their nutrition and training programs… and he just kept insisting: “Playoffs, playoffs, playoffs!” ?

Engineers and programmers – the exact professionals who are inherently more qualified than anyone else to judge the nature and structure of designs – are sick and tired of this. They smell a rat.

Old-school Darwinists put us down for failing to submit to scientific consensus.

But we engineers know that we know that we know certain things.

For quite some time I was tempted to dismiss evolution. It didn’t make sense to me that any sort of random, undirected process could generate the amazing systems we find in living things. But I chose to suspend judgment. I scoured hundreds of books and papers. Including many books I disagreed with, like Jerry Coyne’s book Why Evolution is True.

Layer by layer, I started peeling the onion. I found real-time laboratory evolution experiments that produced new features, new species.

Barbara McClintock asked, “What does the cell know about itself?”

Great question. And what engineering capabilities does it have?

We are barely beginning to find out.

Meanwhile, chanting “natural selection” as though it’s some oracle or magic incantation is sheer laziness.

So is critiquing books you’ve never bothered to read.

Dear reader, I invite you to read my book Evolution 2.0 and discover the real evolution story.

Maybe you’re an old-school Darwinist. Maybe you always felt like the basic evolution story makes sense. If so, you’ll probably find there’s far more sophistication to evolution than you ever imagined.

Maybe you’re a creationist. If so, this book has an excellent chance of convincing you that some form of evolution really does happen. Three of the endorsements in the front matter of this book are from creationists who literally changed their mind about evolution. They “flipped.”Evolution 2.0

Maybe you’re sympathetic to Intelligent Design. This book will show you things the ID guys probably didn’t tell you about.

Maybe you wonder about this alleged war between science and religion. This book will show you there’s no conflict.

Darwinists underestimate nature. Creationists underestimate God.

Get yourself a copy (Hardcover or Kindle). READ IT FOR YOURSELF – think for yourself – and decide.

Perry Marshall

Photo by zooterkin – Flickr: P1080729 from Wikipedia used under Creative Commons License.

 

36 Responses

  1. Jimmy Snyder says:

    Mr. Marshall write: One of reasons I wrote this book was to show precisely those kinds of people that evolution is still, in fact, true!

    I am reading a textbook on biology entitled “Molecular Biology of the Cell” by Alberts et al. I think it’s aimed toward undergraduates, but I’m not sure. It makes extensive use of evolution in its explainations. Yet at no time does it ever say that evolution is true. As you might expect from real scientists, the theory is used as a tool in order to understand the data coming out of experiments. A hammer is a tool as well. I can understand people sitting around and arguing about whether a hammer is a useful tool. But is it true? I mean is a hammer true? What kind of question is that? Not a scientific one. The scientific question is “Is evolution useful as a tool to understanding?” Questions like “is it true?” do not belong in a scientific discussion, only a philosophical or religious one. Not that there’s anything wrong with that. By all means have such discussions and let them be good ones. But don’t barge into a scientific seminar and ask everyone to stop doing science for a while because you would rather do something else.

    • Jimmy,

      Thank you for your question. If you read *widely* on this topic you will see that skepticism about the claims of Darwinism runs far outside of religious concerns. If you want an outstanding classic example see “Evolution Under the Microscope” by Swift. There are many, many others.

      I relate to people who are skeptical about evolution itself. Why? Because the specific model proposed by classical Darwinism is mathematically impossible. It is not possible for DNA copying errors combined with selection to produce endless diversity of more and more species – because copying errors destroy information. Nobody knows this better than an EE educated in information theory. I wrote an Ethernet book. Noise always destroys information and random mutations are noise.

      Of course people with religious views are much more likely to raise these objections; but they are not alone. Classical Darwinism is the most conflicted theory in the history of science.

      Fortunately for the practice of science, modern microbiology and Systems Biology have shed a great deal of light on the mechanisms of evolution. These fields have come to the rescue of evolutionary theory. They are not random, they are not accidental. Transposition, epigenetics, Horizontal transfer, symbiogenesis and hybridization are all extraordinarily sophisticated systems and adaptations that are performed by the cell’s built-in adaptive machinery.

      All of this is Post-Darwinian and all of this is very scientific and exhaustively demonstrated by experiment. All competent biologists know about these things. The public does not.

      However people like Jerry Coyne don’t like to talk about this stuff very much because none of it reinforces the idea that the universe is some random, purposeless place. In fact it sort of suggests the opposite. Coyne wants to change the subject. And I’m not letting him do it.

      Again I’m only reporting what 70 years of research clearly show.

      So when I present this information to people who are skeptical about evolution, usually their skepticism melts.

      Scientists are happy to see this happen – and you see my book is endorsed by a number of mainstream scientists. Atheists, however, are not so happy. So ironically I’m endorsing evolution and I’m explaining to people exactly how and why it works – I’m not just waving a magic wand called “natural selection” – and Jerry Coyne is mad.

      He should be. Because his outdated, “natural selection is the only game in town” model is finished. Just like “Junk DNA” is finished.

      Don’t take my word for it. Just look up the systems I mentioned above and see for yourself.

    • Joran says:

      I get what you’re saying here, but I think it’s more caught up in the language used than the message conveyed. While maybe not worded in the most accurate way, we understand what he means about evolution being “true”, similarly to how we understand what you mean by “doing science”.

  2. Jimmy Snyder says:

    Except for the part where you prejudge just how *widely* I read, I find nothing to disagree with in your post. However, it completely avoids the issue in my own. I take disagree with anyone who describes any scientific theory as being true, not just evolution. A single experiment can falsify a theory, but no number of experiments can ever truthify one. Can you justify your use of the word true in the following quote of yours?

    “One of reasons I wrote this book was to show precisely those kinds of people that evolution is still, in fact, true!”

    • If a theory says that organisms can develop observable new adaptations by some mechanism in real time, that theory can be verified and all the mechanisms I described fit the bill. I describe the experiments and provide references. I find this is very effective with evolution skeptics. I also find it effective with old-school Darwinists (so long as they’re willing to listen).

      • Bert says:

        The statements, discussions and arguments make for an exercise in academic discussion – and to some extent an exercise in futility.
        It should be evident by now that creationists hold a particular view about life and no amount of logical discussions is likely to sway their belief one iota.
        Scientists and those with a science background are usually uncertain and are therefore willing to learn. The use of the word “true” is something scientists are likely to use sparingly, since truth is not as dynamic as we may like to believe.
        Evolution certainly does not explain everything but Religion which is more or less synonymous with creation has no answers.

    • heather angus-lee says:

      Mr. Snyder: I honestly didn’t know that “no number of experiments can ever “truthify one [a theory]. Isn’t that what the intention and achievement of science experiments have done? please explain what you meant. sincerely confused. thanks

  3. Joe Brinkman says:

    I’m trying to understand this and not sure where to post this question.

    When I cut down a tree, I see rings. Those rings tell me, in detail, an incredible amount of information about the history of that tree. It’s lifespan, nutrient content at various stages, disease, trauma, growth rate, etc. Is this not a naturally occurring code? It is stored information in nature. If you object by saying there is no obvious way to decode it, then you are adding a new requirement to your challenge, and I could retort by postulating that man exists for the sole purpose of decoding tree rings, which you cannot objectively refute.

    As a believer and a fan of GK Chesterton 😉 I find the code argument incredibly flimsy. Go ahead and set me straight by all means.

    • Joe,

      You can easily answer this for yourself by referring to the instructions at http://www.naturalcode.org.

      Draw the tree rings and put them in the context of a communication system. Label the initial message, the encoder, the transmitted data, the decoder and the final message. Label all ingredients in the system.

      And by the way you can’t use a tree because a tree is a living thing and the requested example of a naturally occurring code necessarily excludes living things. (Your argument presumes in advance, with no proof, that trees and man are an automatic result of purely physical processes. We do not know where living things came from.) Remember, you’re trying to prove that a code can naturally occur OUTSIDE living things. So you can use layers of sediment or arctic ice instead if you wish.

      If you go through the process of diagramming this to a formal communication system, I believe the code argument will forever cease to be flimsy for you.

  4. Joe Brinkman says:

    Perry,

    Using an ice core works fine. Ice cores contain historical data that describes the atmospheric makeup of their place going back hundreds of thousands of years. This data is contained in various forms, most notably trapped gasses and dusts inside the ice. Requiring a “decoder” for this ice, while barring the use of anything you would accept as a valid decoder by barring all living things, is you doing exactly what you forbid: presuming the argument in advance.

    However, assuming I choose to play your game, the act of decoding something is merely changing the information from one form to another. Which form represents a “code” and which form represents the “decode” is arbitrary. Every time light passes through these sheets of ice, the data trapped therein is decoded and re-coded into the light waves as they pass through. This is because different gasses reflect, refract, and block light in different ways, as do different dust particles. In essence, the light is decoding the ice cores at all times as the information now exists in a new form. This light then transmits this coded information into rime ice, or whatever the first opaque object it hits is. The information is now re-coded in multiple forms, those forms being shadows, melting effects, changes in particles structures, and so forth.

    I could make the same argument in perhaps a cleaner manner by using gravity or even black holes in my example. Gravity is constantly transmitting the location of every object in the universe in a coded form to all other objects in the universe (albeit very distant ones to an infinitesimally small degree). These locations are then felt by other bodies which decode it by altering their trajectory, and then re-encoding their new positions in real time and sending the information out to every other body in the universe. Code, decode, recode.

    I won’t get into black holes as I feel it is unnecessary for this argument. While it’s certainly true that God very obviously exists, to me the code argument reeks of semantic sophistry.

    • Actually the act of decoding something is not “merely changing the information from one form to another.” It is a mapping of one symbol sequence to another. You probably are not familiar with communication theory but if you do as I requested, work the diagram and try to formally meet the spec of the prize, you will see this is much harder than you imagine. None of these scenarios you describe involved any digital encoding or decoding of any kind.

      • Joe Brinkman says:

        You impose a ridiculous number of arbitrary requirements in order to box your opponent in. In doing so, as I said before, you are presuming the argument.

        Requiring digital encoding is yet another arbitrary rule; you might as well stipulate that, in order to disprove you, someone must discover naturally occurring DNA, that is not alive, but is also undergoing self-replication (which would probably disqualify it as being alive, if I’m starting to understand this particular brand of sophistry). I’m sure viruses have been mentioned, since they fit all of your requirements perfectly but have the disadvantage of using RNA – which I’m certain is too similar to DNA for your liking to be considered. What you want is something that is both identical and different.

        You’re in good company with Ahab on this quest. I only hope it ends better for you.

        • Joe,

          The reason for my stipulations is that DNA transcription and translation is a formal encoding/decoding process. This is not sophistry, nor is it “ridiculous.” This mathematical rigor. I understand your frustration, but understanding DNA as code – and the question of how to derive such systems from purely physical processes – is not nearly as simple or easy as refracting light through layers of ice or something like that. Nobody understands this better than a person with a degree in Electrical Engineering and a specialty in communication systems.

          If you are interested in this subject read Hubert Yockey’s book “Information Theory, Evolution and the Origin of Life” (Cambridge University Press 2005).

          I frequently get emotional reactions like this — incredulity that I would raise the bar so high. As well I should. We are doing empirical science. Just-so stories about lightning strikes in warm ponds creating life once upon a time are nothing more than stories. If you want to explain the origin of self-replication, you have to stipulate all the major elements. Hand-waving explanations will not do. Again, Yockey’s book makes this quite clear and I recommend that you read it.

  5. Joe Brinkman says:

    In all seriousness, Perry, a God-fearing man who is good for his word should be jumping to give either myself (or whoever first pointed out RNA viruses) the oft-touted prize money. It very clearly fits every requirement you lay down. However, as with everything, you will object that you cannot be certain it occurred naturally (am I right?). Or will you contest that viruses are alive? In any case, I’m sure all of your definitions will neatly protect your circular reasoning.

    You haven’t “raised the bar high,” and I now understand why your brother stopped arguing with you and adopted agnosticism. I would have done the same in your presence. Your pride (or is it fear of loss) blinds you to reason. All you did was lift the bar (encoded information) just-so, and lowered the bar above it (living things) just-so, such that both bars now touch each other and there is no room to squeeze anything between them. Either you are intelligent enough to see this and are scamming people while claiming to be a believer in God, or you are hopelessly caught in a web of your own making.

    I wouldn’t be concerned if I didn’t get the sense that this argument defines a significant part of who you are, as well as the structure of your life. For those reasons I understand why you are unable to cope with counterarguments but must instead tighten the vice grips that hold those two bars ever closer and closer together.

    If you are ever interested in a real argument for God, let me know. Until then, you may chew on this: If God created us, and did so through DNA (which in your mind proves God exists), doesn’t it seem sadistic for the grand revelation proving the Creator’s existence to require advanced instruments of science and the discovery of DNA and communications theory? Why would God arbitrarily withhold his “proof” from man until the information age? The truth is that the real proof is far less problematic than this slipshod code argument and has been available since the first rational thought entered the first brain of the intelligent mind, available for all in every place and in all time.

    • This doesn’t prove God. Sure, it does infer a designer, but I think the most valuable thing here is for someone to empirically demonstrate how the first codes could have come into existence. Personally I believe that it is obvious to everyone that nature itself comes from something very great and majestic, regardless of what century they were born in. St. Paul says the same in Romans 1.

      The reason that I have a sophisticated prize and specification for origin of information is that we do know more than ever before about codes, information, DNA and life. You have not in any way satisfied the requirements of the prize, and I do not believe you understand them. The first step would be for you to go through the prize specification line by line and show how layers of ice satisfy the requirements. When you go through that process, you will begin to understand the size of the challenge. Again I recommend Yockey’s book, he lays the groundwork superbly.

      This debate has a very long history going back 10 years and you can read all about it at http://www.cosmicfingerprints.com/infidels.

  6. Joe Brinkman says:

    I’ll add the final note that you have not disproved why RNA viruses don’t fit your requirements. Twice now I’ve mentioned them and both times you’ve skirted them (the second time reverting to the ice core reference where I clearly eschewed it to satisfy more of your requirements). I can arbitrarily define viruses as not living (many consider them so), naturally occurring (many consider them so), and capable of replicating in the appropriate environment just as DNA does. RNA and DNA are not the same thing. I can arbitrarily define them in any way I like to fit your requirements and there is not a single objective thing you can do aside from backpedal or pile on more requisites. You’ve added to your list of requirements “the origin of information,” in your most recent post. This was worthy of a chuckle.

    You view digital information like a CD or a flash drive, floating around the Earth magically created and replicating itself as out of a fairy tale. This view, which is starting to come into focus for me, illuminates your apparent delusion. Perhaps all intelligent life is humanoid. Perhaps all stars are spherical. The urge to twist such observations into a perverted argument for God is a scourge on humanity. This is because it is flimsy arguments such as these that many atheists will be exposed to and (rightly) reject, many who could be brought to the truth are lost because once they reject God, they don’t often open up to the idea again. But hey, you sell some books and ads, so its all good, right?

    Keep your arguments to your own moderated site and atheistic sites where it bears little rigor. That’s my advice.

    • Joe,

      Your “Ahab” remarks are snarky and insulting. Keep it civil.

      You have not proven the origin of RNA viruses, and furthermore RNA viruses need the machinery of other cells to encode and decode. To present any form of life as your evidence is technically defined as “begging the question” – attempting to prove a proposition based on a premise that itself requires proof.

      Origin of life theories presume that cells and information such as we find in DNA can emerge from purely material processes. If you wish to prove that, then you have to start with a purely material process (not an existing life form) and show that it can generate communication systems. If you can do that, you win the prize.

  7. Joe Brinkman says:

    RNA viruses are disqualified because they require DNA machinery. That’s rich. Are you now going to claim that DNA does not require the machinery of the natural world to survive? Things like warmth, an atmosphere, gravity, strong/weak nuclear forces, and on and on? I came back to read out of morbid curiosity but this was depressing.

  8. John M says:

    Hi again Perry! This is JohnM from sometime ago…

    Your work has really helped me a lot! One of the questions I haven’t been able to quite put to rest is….once we infer mind as the cause for information based on 100% of our observations, can it not be said that minds based on 100% of our observations only function in physical “bodies”? How can I point to a immaterial code Maker when all our observations infer minds only exist in biological bodies?

    • John,

      First and last name at all times, please, from now on.

      While we can obviously infer an immaterial mind, we can’t prove it.

      Actually this issue is not terribly different from the principle that life ALWAYS comes from life, no known exceptions, so science has no answer for Origin of Life. So we absolutely have no choice but to venture outside of what is known in order to answer the question. At that point it becomes a question of which is more absurd – a material cause? Or a metaphysical one? All of the thinking of philosophers about the mind/body problem over millennia comes into play.

      Meanwhile I have a $3 million prize for the first person who brings a workable material cause to the table.

  9. John May says:

    Hi Perry, in a discussion I was asked, “If DNA is such a code, then tell me how amino acids (the building blocks) are produced without it within asteroids? If DNA is the code, then amino acids are the carriers (RNA). How can there be carriers if the DNA didn’t tell them what to carry or what kind of carrier it would even be?

    http://news.nationalgeographic.com/news/2010/12/101220-asteroid-meteorite-life-space-science/

    Not sure how to answer this. Does this pose a difficulty for the DNA argument?

    Also its been a couple of years since I really kept up here….since then how do you feel the argument has done? Stronger? Weaker? the same? Any additional findings in support of your argument that might help me?

    Thanks!

    • That’s like saying “if Microsoft Windows is code running on a Pentium chip, then how come we can find silicon in rocks on the moon?” It shows the person you are talking to doesn’t know what we’re talking about.

      This argument had a few fuzzy edges 10 years ago. It’s rock solid today. I put a $3 million prize behind it, after all. http://www.naturalcode.org.

  10. John May says:

    Thanks! In a discussion I tried to explain how the base pairs have no particular attraction pertaining to sequencing etc… that they are like magnet letters on a fridge, someone has to put them in a meaningful sequence to make words, sentences etc. In support i posted:

    “Meyer explains,

    Kenyon and Steinman had shown that certain amino acids form linkages more readily with some amino acids than with others, new studies showed that these differential affinities do not correlate with actual sequencing patterns in large classes of known proteins.[3]

    The individually weak hydrogen bonds, which in concert hold two complementary copies of the DNA message text together, make replication of the genetic instructions possible. But notice too that there are no chemical bonds between the bases along the longitudinal axis in the center of the helix. Yet it is precisely along this axis of the DNA molecule that the genetic information is stored.[4]

    Explaining DNA’s information-rich sequences by appealing to differential bonding affinities meant that there had to be chemical bonds of differing strength between the different bases along the information-bearing axis of the DNA molecule. Yet, as it turns out, there are no differential bonding affinities there. Indeed, there is not just an absence of differing bonding affinities; there are no bonds at all between the critical information-bearing bases in DNA.[5]

    To which they replied…

    “There are two things here that you seem to have confused. One is that molecules capable of replicating exist, and the other is about the mechanism of heredity which those molecules implement.

    The article claims

    “But if the combinations are equal, then why would certain patterns of information emerge?”

    and this is entirely asking the question why certain orders of base pairs and not others, and was nothing to do with the fact that base pairs have a deterministic chemistry totally predicated by their electronic properties. The thing is, the question answers itself. Why that sequence? Because it’s the sequence that leads to preserving the sequence. If it wasn’t, it wouldn’t exist. So in fact, combinations are not equal – like the Game Of Life, some lead to stability, some lead to new behaviours, some lead to cul-de-sacs, some lead to oscillations.”

    To me this sounds like what makes it makes it….thus the sequence that works, is the one that passes on. Im kinda confused here….

    Also im presented with this… http://www.examiner.com/article/dna-is-not-a-code

    This fails also doesnt it having no sender/reciever/decoder correct?

    I also stated “The function of DNA is governed by arbitrary codes that cannot be derived from the laws of chemistry and physics”

    They replied “Citation? (Note: peer-reviewed respectable journals only please, not books, not Discovery Institute, not discredited Intelligent Design pseudo-science, this should be easily found if it’s true).”

    I cant find who originally said that do you recall?

    Thanks sorry for lengthy, just trying to work this through,

  11. Sam Platt says:

    “Sure, it does infer a designer, but I think the most valuable thing here is for someone to empirically demonstrate how the first codes could have come into existence.” – Enough with the “code” already Perry. DNA is a molecule. DNA is not a code. It is analogous to a code, yet it is not a code. It is a molecule doing what molecules do. Let’s move on, shall we?

    • Yes, if you wish to move us back to before Watson and Crick discovered the genetic code, and discard the entire profession of bioinformatics, then sure we can “move on” – back to the 1950’s.

  12. Jan Bernhard Haarhuis says:

    New light through old windows, the tittle of a Chris Rea CD !
    The same with Evolution 2, where the dogmatic darwinists and creationists “create their own belief, as a kind of established religion!”, or better more or less a “new inquisition”, only now it,s impossible for them, to “burn you at the stake !”. As Dr. Stanton Friedman showed in his book “Science was wrong”, which should be a good mirror for those who think that “everything already is known”, or “Don,t border me with the facts, I already made up my mind, like Mr. Coyne”. No matter WHERE the DATA leads you, you have to investigate. That,s into the CODE the DNA is ! Nothing here is random, that,s the amazing enigma of it . More reseachers are coming in from different fields of science, “out of the box”, thinkers who eventually will prove, not only who created the DNA CODE, but also WHERE human beings are coming from. Now we explore our solar system, our planets, where we already have evidence by pictures, cq. the data, WHAT the government is hiding for the public.
    Humans will land on Phobos and Mars, and the moon again, to investigate once more the “The unbelievable wonders out there
    for those who can remove some of truth protecting layers !, As Neil Amstrong spoke !. The mystery will be revealed at last, it takes “cosmic time”, for us, and MAYBE ( this is only a guess), our human goal and destiny is made up in our genes/DNA to undertake this quest, and at last “To touch the face of the Gods !).
    Newton,s laws of motion aren,t correct afterall, as Dr. Bruce de Palma showed in his spinning Ball Experiments ( as Nazi scientist Wernher von Braun already knew !). The speed of light can BE EXCEEDED. Spacetime is not curved as Einstein said. Nobody understands quantum mechanics. It only works if you don,t include GRAVITY in the mathematical equations. Nobody can tell us WHAT gravity is ( maybe also good for a fair prize ?). It,s the outside force that matters, this is the fourth physical dimension ! Mr. Perry you are an electrical engineer, and it all started with James Clerk Maxwell. Our universe is hyper dimensional ! Maxwell knew this already, and had to create a fourth spatial dimension. He used special numbers the socalled: “: quaternions”. There is no dark matter or a fixed speed of light. no zero point energy, or super strings.. All the energy is coming from he dynamic torsion, outside our
    3-D Universe. We will learn more and investigate our planets, e.g. Mars. Dr. John Brandenburg wrote a book about it, The nuclear Massacre on this Red planet. Humans will dig there in the future, for sure. and don,t say “this is all a fairytale. We wll learn about our ancestors in the cosmos. NASA knows, ESA knows what MUST be there, waiting under the cydonian sands. No,no red marsmen, but what must have been an amazing humanoid civilization.
    There and elsewhere we will find the artifacts, maybe about the DNA. and our origin of the ” creation of the human being”, and maybe the discovery of the Super being, or whatever you want to call it, “God, The Maker, the great divinity. But don,t enter into dogma.s,…they will cover your brain and spirit…out human spirit to investigate, and as Perry wrote: ” The origin of live has all indications of being a deliberate, astonishing act of OUTSITE INTELLIGENCE, a MIRACLE, you could say.

  13. Bart Nielsen says:

    Hello Perry. In the unicellular world can you show an example of a population of,say, bacteria that have transformed into a different family of bacteria? This needs to be something like going from Gram negative to Gram positive. Picking up the ability to metabolize citrate does not make every coli something other than ever coli that metabolizes citrate.

    After that if you could point to some multicellular organisms that have crossed the barrier of kinds (e.g. dogs to cats, that would be great. Thanks.

    • Quoting from Evolution 2.0 page 129:

      Dr. Kwang Jeon, a professor at the University of Tennessee, did an experiment where tens of thousands of bacteria took up residence inside Amoeba proteus organisms. A fierce parasitic attack ensued, killing almost all the amoeba. But in the space of a year, amoeba and bac- teria entered into symbiosis. Both modified expression of their genes as necessary, to support the mutual dependence (624, 636, 653, 652).
      Jeon learned how to reliably trigger symbiotic cell mergers between amoeba and bacteria. It took 200 generations, about 18 months, for the cells to become fully interdependent. After that, removal of either symbiotic partner proved fatal to both (625).

      Real-time symbiotic merger. REF http://www.ncbi.nlm.nih.gov/pubmed/15537083

      Crossing the barrier of kinds:

      Evolution 2.0 page 137

      Bread wheat, for example, came from blending emmer wheats with goat grass, a noxious weed, meaning one of the world’s most popular crops came from blending a moderately useful crop with a useless pest (673).
      An article in ScienceDaily titled “Two Species Fused to Give Rise to Plant Pest a Few Hundred Years Ago” (679) documents how a fungus originated from a hybrid 380 generations in the past. The researchers identified specific transpositions in the hybrid’s doubled genome that stabilized into a brand new, stable species.

      https://www.sciencedaily.com/releases/2012/07/120703133725.htm

  14. Erik Strandness says:

    Hi Perry, I’m a neonatal physician. I was involved in basic science research for several years before I entered private practice. I am appreciative of the perspective you bring as an engineer. Physicians and biologists take apart things to see how they work. Engineers on the other hand actually build things. A biologist looks at science completely different and doesn’t have the perspective to see just how difficult it is to build a complex information processing system. Your book helped me think about this issue in a completely new way. Thank you for bringing your expertise to bear on this question and challenging scientists to become better scientists.

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