PZ Myers – Perry Marshall Debate Evolution on Podcast

Atheist PZ Myers Debates Perry Marshall 

Darwinism vs. Evolution 2.0 on “Unbelievable?”

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Host Justin Brierley: Welcome to Unbelievable, the show that aims to get you thinking. Today we’re asking the question “Is it time to upgrade to evolution 2.0?”

Perry Marshall is an author, speaker, engineer, and world-renowned business consultant. So why has he written a book on evolution? Well, in Evolution 2.0 Perry claims to have found a way to break the so-called deadlock between Darwin and Design.

The book includes information on how organisms re-engineer their genetic destiny in real time. It talks about the amazing systems that living things use to redesign themselves, how every cell is armed with machinery for editing its own DNA, and much more.

And Perry’s even offering a public award for anyone who can answer the greatest question in all biology, he says, ‘Where does genetic information come from?’

We’re going to meet Perry in a moment’s time. But opposite him on the show today is PZ Myers. Well-known as an atheist biologist, who’s not afraid to speak his mind on his popular blog Pharyngula.

He regularly critiques the Intelligent Design community and has denounced Perry in the past too, though Perry doesn’t claim to be Intelligent Design. And we’ll get to that a little later. He’s had a chance to look at Perry’s new book and is going to be addressing Perry’s claims, so welcome both PZ and Perry to today’s program.

Perry, let’s start with you. This book is sort of the journey of ten years, more or less. Do you want to tell us about that journey, and why you, in the end, became dissatisfied with both Intelligent Design and Darwinist camps in this debate?

Perry Marshall: This started when my younger brother, who has a master’s degree in theology, was a missionary in China, and in the space of 4 years became almost an atheist. We’re very close, and there were emails and emails back and forth for a couple years, and one day I’m in China visiting him.

We’re sitting on this bus, and we’re having this argument number three hundred and twelve, and this has been going on a trajectory, and he’s very smart. I just was feeling like I was losing ground, and I found myself grabbing for science.

And I said “Bryan, look at the hand at the end of your arm. You don’t think this is a long series of accidents that produced this do you?” “Well, actually yes I do.” And he kind of pushed back with a Neo-Darwinist view of things. And I knew two things: I knew yes I did have my engineer’s intuition about this.

On the other hand, I knew, without him even telling me, that most biologists would be more inclined to agree with him than me. I knew I didn’t know.

I have an electrical engineering degree. I knew that there are things in engineering and in science that are powerfully counter-intuitive. And I knew I didn’t know. But what I did know was that engineering and science are a lot less ambiguous than theology. (Laughing) PZ might agree.

And I said ‘you know what, I’ve got the same question Bryan has. I’m going to let science settle this for me.’ And I went down the rabbit hole.

I’m an obsessive person and I bought probably 200 books. I started reading scientific papers, and I said I’m going to get to the bottom of this, I’m going to find the truth of this. And I think it’s probably going to inform where I go in the faith department.

For a while I just floundered helplessly. I would listen to both sides and all I could decide was: I’m not going to ignore any verifiable fact. And I’m not just going to learn “my side” or whatever the party line might be. I’m not even sure what it would have been anyway. I’m just going to take all the information and try to touch the bottom of the swimming pool at some point.

It was very unsettling at first. The waves would toss back and forth. Both sides kind of made sense and both sides didn’t.

There was a point where I first touched the bottom of the swimming pool and it was recognizing that: because I had written an Ethernet book in 2002 for a major professional society called the ISA which was for process engineers, I knew how 1s and 0s work, I knew how code works, and I came to realize that all of the math, and all of the principles of code, apply to DNA.

Now DNA is code. Cells are more than code, but at the very minimum the principles of communication applied to the cell, and now I could begin to break this apart. And I realized: evolution is a software engineering question. At least I can make a substantial amount of headway starting with that.

And I found a tremendous body of literature connecting genomics to communication theory. And there are journals on bioinformatics. Then things began to make sense. Now to fast forward the story quite a bit more, so we can get into this discussion.

I realized that error correction and error detection were absolutely critical to any kind of communication process and any kind of DNA replication.

Yet the Darwinian view was that random copying errors, among other things like population genetics and gene flow and things like that, were major drivers of evolution. And that it was inevitable that copying errors and things like that would inevitably produce new structures, new organs, new features; natural selection would select them, and that you would have constant improvement just naturally with time.

But everything I knew about software said software doesn’t work that way. And having written an Ethernet book, copying errors never – for all practical purposes – they never help.

So I had a giant discovery moment when – let me just say that for a while, I’m looking at evolution, I find lots and lots of anecdotal evidence that there is evolution. I don’t think the creationists are right on this. I don’t think this is all fake.

However the mechanisms they’re telling me about don’t make sense mathematically and engineering-wise. And then I discovered the work of Barbara McClintock. And her story is:

She kind of approached problems like a hacker. She was hacking corn plants in 1944 using varying measures of radiation. And she damaged a chromosome of a plant. And the plant threw her a curveball; it did something she totally did not expect.

And if I might use an analogy, what she had done was she had ripped a page out of a novel. So if you could imagine ripping a page out of a novel, giving it to one of your friends who’s a writer: “I want you to fill in the missing page by reading what’s before it and after it and use words and sentences that are already in the novel and make it all make sense.”

And this is essentially what the plant did. She called this transposition. Certain genes were moving around and changing the expression.

Host: It kind of re-wrote itself. It sorted of repaired itself at some level.

Perry: Yes, the cell repaired it; it rewrote its own code. She presented this at a symposium. Half the people there laughed at her. And the other half were angry. They were like ‘who does this women think she is, suggesting that plants can re-engineer their own genetics?’ And they didn’t accept i

Barbara McClintock discovered Transposition, which changes expression of genes by moving Mobile Genetic Elements in your DNA. This is similar to the way English changes when we re-arrange words.

If you transpose the sentence “you did have coffee this morning” to “did you have coffee this morning,” you change it from a statement to a question.

 

Well in 1983 she won the Nobel Prize for discovering transposition. And I believe that what she really had done was she was one of the very first scientists to observe evolution actually happening in real time and understand genetically what happened.

Host: Obviously this is just scratching the surface, which you delve a lot deeper into in the book.

But essentially what I take away from this is you develop this view which you say is simply bringing to the surface all this science that’s already out there, but essentially not talked about much in the public sphere.

That essentially there’s a sort of, for want of a better word, intelligence in the cell.

There’s a purposiveness in what the cell does, it’s not just a case of, as you say, random mutations naturally selected over a long period of time. There’s a sense in which the cell is doing a lot more than we ever gave it credit for, in that sense

Symbiogenesis a cell merger-acquisition. A chloroplast is algae inside a plant cell. Epigenetics switches genes on and off in real time. Ohno’s Hypothesis says genome duplications formed vertebrates in hybrids. Horizontal Gene Transfer exchanges DNA between cells.

The Intelligent Design community talks about “Irreducible Complexity” – systems that don’t work unless all the parts are in place. But McClintock proved cells perform sophisticated, irreducibly complex operations in minutes. She talks about rapid new species via hybrids for example. So unlike what Darwinists say, evolution isn’t always gradual. Isn’t fast evolution in live experiments a lot more intriguing than saying it’s impossible?

 

Perry: Yes, they are most emphatically non-random. They’re anti-random, in fact, I would say. So now evolution began to really make sense. And Barbara McClintock was only the tip of the iceberg. Then there was the work of Lynn Margulis on symbiogenesis. There was Ohno’s 2R Hypothesis. There was Epigenetics. And Horizontal Gene Transfer.

And when taken together, these mechanisms actually explain what’s going on, and you can observe them in real time. And I thought this is so much more interesting than what the Intelligent Design guys are talking about, and this is so much more interesting than the traditional Darwinists are talking about! Why isn’t anyone talking…?

Host: Well we needed to take some time to explain where the book came from and the central thesis behind it, so we can begin this conversation now with PZ.

PZ, you’ve run into Perry’s work before. You’ve not been very complimentary about it. So what’s your take on Perry? Do you think he’s just recycling Intelligent Design perspectives? What’s your take? 

If I were in PZ’s position of defending an outdated theory against an outsider, I would also pat the guy on the head and accuse him of not really understanding what’s going on.

But PZ shows poor understanding of Transposition. He makes false statements like “there was absolutely nothing in McClintock’s work that argues against the importance of chance in this business.”

Don’t take my word for it. Read or watch McClintock’s Nobel Lecture. Notice near the end when she talks about rapid “punctuated evolution.” You don’t need to know the stages of cell division to ask: Does anything she’s talking about sound “random”? Is PZ accurately representing her work?

Fact Check: Transposition is when the cell moves a defined cassette of coding sequences and plugs it into a new location. [The “cassette” link shows transposition cassettes in experiments with zebrafish]

Transposition is not just inserting unspecified DNA sequences. Transpositions are by their very structure non-random, and would be even if there were no pattern to where insertions occur.

There almost always is some pattern to the insertions. Yeast retrotransposons insert either >95% upstream of transcription start sites (Tf1, Ty1-Ty4) or >95% into silent chromatin (Ty5).

Contrary to what PZ said, McClintock’s work is explicitly about cells engineering solutions! That is her point. The name of McClintock’s 1983 Nobel Prize speech was “The Significance of Responses of the Genome to Challenge.”

From the first paragraph of her Nobel speech (emphasis mine):

“It was necessary to subject the genome repeatedly to the same challenge in order to observe and appreciate the nature of the changes it induces… In contrast to such “shocks” for which the genome is unprepared, are those a genome must face repeatedly, and for which it is prepared to respond in a programmed manner.

“Examples are the “heat shock” responses in eukaryotic organisms, and the “SOS” responses in bacteria. Each of these initiates a highly programmed sequence of events within the cell that serves to cushion the effects of the shock. Some sensing mechanism must be present in these instances to alert the cell to imminent danger, and to set in motion the orderly sequence of events that will mitigate this danger.”

All her examples (SOS etc.) trigger transposition.

PZ doesn’t appear knowledgeable about McClintock’s work. Her findings perplex Darwinists because Darwinism has no grid for cells re-engineering themselves… but that’s exactly what they do in experiments.

The real problem here is not that PZ misrepresents transposition. The real problem is: Any time you declare “it’s random,” you hit a scientific brick wall. There is no more order or structure to discover. “Randomness” kills curiosity and prevents scientists from doing their jobs. It becomes a self-fulfilling prophecy.

The only way a scientist can discover anything is to NOT assume randomness, but assume there’s a pattern. That’s what McClintock did and it’s why she won the Nobel Prize.

PZ is correct in describing biological systems as “Fault tolerant.” Tolerance to faults is by definition non-random. Cells are fault tolerant because are able to protect and modify their DNA in pursuit of those goals. Notice PZ says “cells hate…” because they do.

 

 

PZ Myers: Well, he’s trying to put a new twist on it, but he’s getting it all wrong. You know for instance when he’s – what I thought was very telling, it’s also telling in the book – he’s a software person, he’s an electrical engineer, and he’s trying to impose his perspective on biology.

So he says ‘ok, biology doesn’t make any sense when I look at it as the way software works’.

Instead of saying well maybe my analogy is totally off base and wrong, he says what we’ve got here is a situation where the biology does not conform to his expectations of how it will work.

And yeah biology is far more fault-tolerant than electrical engineering. You can’t directly compare it to software or code or anything like that because it’s got a lot more complications going on with it.

But on top of that in his book what he tends to do is throw out science buzz words like ‘transposition’ and the transposition discussion is a good example of this. He throws them out, but he doesn’t really understand them.

He’s got McClintock totally wrong. McClintock’s work, which was marvelous work, and yeah it was not initially accepted because it was difficult stuff. If you read her papers, she’s got an amazing mind, it’s really complicated, really difficult things to understand, and that’s largely why it wasn’t immediately accepted.

But she was very convincing because she brought the data to bear. But all of her work was on something called genetic instability, ok? It’s not about cells engineering solutions.

For instance, the stuff on bridge break fusion that Perry mentions. That’s about random chance breakage of chromosomes that have exposed ends. They tend to re-fuse and then when mitosis and meiosis occurs they break. And they break in random places.

Not in designed, engineered, planned places. But in an entirely random way which means that the progeny of that cell will exhibit greater genetic variation than the parent.

There was absolutely nothing in McClintock’s work that argues against the importance of chance in this business.

Host: Can we maybe start to open up that area, before we progress onto any more. Just from the point of view, you’re saying, PZ, base: the analogy is all wrong–Perry’s come to this as an engineer, well this isn’t computer engineering that we’re talking about, this is biology. Very different thing. Different types of tolerances, different kind of thing going on.

And then you’ve obviously got specific criticisms about how he’s interpreted that particular work that he spoke about.

Ok, the obvious question that PZ has aired here: Perry is an engineer, so why, no matter how good he may be at engineering, is he writing a book on evolution? You aren’t a qualified scientist in that sense, and a lot of people will probably throw your claims out the window just on that basis alone.

Why do you believe an engineer does have the right to throw his hat into this ring?

Perry: We build models in science. And all scientific descriptions are models. All scientific descriptions are analogies. If I drop a steel ingot off the building onto the ground I can use calculus to calculate its trajectory. But the calculus is not a steel ingot and its gonna have a margin of error.

The question at hand is: do the models of information theory apply in biology to the rearrangement of code? And we have huge bodies of literature going back to the 60s that say: Yes it does.

Host: That DNA is an information code. It is not simply like an information code. It is an information code.

Perry: Yes, and I would certainly acknowledge that it is more than a computer program, but it is not less than a computer program. And the rules of information, entropy and all of that work.

Now PZ said biological systems are much more fault tolerant. The reason they’re more fault tolerant is because they have layers and layers of error detection and error correction. So when radiation damaged the chromosomes, the plant repaired the chromosomes non-randomly.

So, yes, the damage was random, but the repair was not.

Host: PZ, why do you think he’s got this research so wrong exactly, can you explain?

PZ: I have no idea, that’s very bizarre, because what’s going on in McClintock’s models are that chromosome ends are broken, and they tend to fuse back together.

Cells hate single stranded DNA hanging out there. So what they’ll do is the two broken ends will stick together. Then when the cell divides and they have to separate, they will break in some random position on the chromosome.

PZ says: “The only repair mechanism here is that it doesn’t tolerate dangling ends”

Transposition does far more than repair dangling ends! Transposition is one part of a very sophisticated programmed response to dozens of kinds of external threats like heat, DNA damage and starvation. Cells re-arrange DNA in highly organized ways.

 

 

The only repair mechanism here is that it doesn’t tolerate dangling ends ok? It fuses dangling ends together. But the actual repair is in essence randomly damaging to the ends of those chromosomes.

McClintock also studied transposons, transposition, which is basically where there’s an enzyme that copies out a piece of DNA and then inserts it into some random other spot in the genome.

It’s a well-understood phenomenon; it’s actually used in a lot of biotechnology techniques. And that again is also a random process.

Often what happens when you have a transposition is that it inserts that copied sequence into a place that’s damaging to the cell, or shifts regulation, or in many cases will be in a totally neutral place and does nothing at all.

Host: Perry?

Perry: There are two problems with what PZ said. One is that error correction in this case is just repairing broken ends. And the latest Nobel Prize discusses three layers of error correction, which result in a copying error rate of less than one in a billion base pairs.

And the correction of the errors is explicitly non-random. Transposition is also non-random because if you get a book on transposition, it shows that transposable elements tend to land in specific places and specific patterns. If you read McClintock’s work on this, what’s going on is explicitly non-random.

Now PZ’s claim that it’s random is not mathematically provable. And what I found was that in every instance when I started chasing things down I would find a pattern, rather than evidence of randomness.

Host: What Perry sees as patterns, do you just see as… I don’t know, what do you see it as PZ if it’s not a pattern and some kind of purposiveness within a cell?

PZ: Well, of course it’s a pattern, but it’s a random pattern.

Patterns can be random. So when McClintock describes the patterns of irradiation and corn, for instance, that are induced by these breakage models of the chromosome, what she was actually seeing is variation in the structure and the color of the tissues that was random. That was driven by random processes.

It’s hard to argue that there was a scheme or a plan behind them. Because we understand the mechanisms for how this was generated. And we can see exactly how it happens, and it doesn’t seem to involve any kind of design elements.

There’s no engineer inside the corn plant deciding where things go.

Host: Okay, you believe that there is some kind of an engineering principle going on. I don’t know if you would hazard to guess how that happens but as far as you can see, Perry, you observe it happening in all that you can tell?

Perry: I predict that there is a mathematical model or matrix that is dictating what is going on. And that that is a testable hypothesis. PZ’s assertion that it’s random is not a testable hypothesis, because it’s not even possible to prove that it is random.

So, PZ, my question for you is how do you know that it’s random and where is your proof?

PZ: So, in biology, randomness is an operational property. What you do is you do the experiment, make predictions about the results you’ll get. And what you typically see in these kinds of experiments is that you can’t predict where the mutation will occur.

For instance, if you’re inducing mutations, you can just predict that it will occur with some frequency. And you do many repetitions of the experiment, and you can get a nice distribution of where mutations occur in each event, you can plot these out.

And you can see that they’re actually fairly random in what they do. That’s all we care about is that there’s a process we can use to determine whether a particular event was predetermined by other prior consequences or whether it seems to be arbitrary.

And in this case when we look at things like transposons, when we look at bridge breakage fusion models. What we see is random variation in an operational sense.

Perry: So, PZ, I believe that you are imposing your view of things onto something and making a statement that you can’t scientifically prove. It’s mathematically impossible to prove that it’s random, so you’re making an assertion that can’t be confirmed.

Now I’ll give you an example of a way that you could confirm that evolutionary events are random, and they are the very popular fruit fly experiments and radiation experiments that have been done since the early 1900s.

If your assertion was correct those experiments would have produced some consistent percentage of fruit flies or moths or bacteria that were better, had better organs. But in fact those experiments didn’t make better fruit flies.

The best they ever achieved was getting the organism to activate its error correction systems; again, which were study of the recent Nobel prize. But those experiments were very disappointing.

Now if you were right, I believe those experiments would have been successful. But those experiments failed to do what the experimenters wanted them to do. Instead what they did was they achieved, they discovered which parts of the genome caused birth defects when damaged.

Which then told the scientists which parts of the genome build certain structures.

Host: Quick response from you PZ, and then we’ll go to break and continue this discussion.

PZ: He was cutting in and out there so I didn’t quite get it all, but I got the gist of it.

Here’s the thing, when we do these experiments what we do see is improvement of the organism. For instance, I work on zebrafish, and I work on a highly inbred strain of zebrafish, and what we find is over time strains of organisms raised in the laboratory become progressively better at living in the laboratory.

Which may mean they are less adaptable, less able to live in the wild. But it’s a routine thing that we see all the time. And under the understanding of ‘better’ as used by evolutionary biologists they fit the criterion.

They get better and better at living in their environment all the time.

Perry: So, PZ, you are taking for granted that this happened randomly, and communication theory indicates there’s no way that those adaptations were random. And my contention is that cells sensing hundreds of inputs from the environment make alterations to gene expression, epigenetics, maybe there’s horizontal gene transfer, there could be all kinds of things.

In the case of your zebrafish, I would think that it’s probably more along the lines of epigenetics and transposition types of events, and this is why the improvements are observed.

It doesn’t just happen with random inputs, it happens because the organism is responding to an input.

Host: Somewhat technical debate today, and we like to do the technical debate sometimes, and two excellent guests to join me for it. We’re asking today: is it time to upgrade to Evolution 2.0?

That’s the title of Perry Marshall’s new book. He claims to have found a way to break the deadlock between Darwin and design. It’s all about capability of the cell to organize itself, to reorganize itself.

There’s something rather special about the cell. It’s not all random mutations acting on natural selection says Perry.

Well, PZ disagrees. PZ Myers is our atheist guest on the line from the States.

[break, reintroductions]

Host: …Obviously what we’re hearing here from Perry, PZ, is as far as he can tell what you describe as randomness, the typical Darwinian-evolutionary model can just as easily, and more easily in Perry’s view, be described as this very purposed response to environment and stimuli and so on. And when we do try and do the experiments where we kind of influence that ourselves, and try to introduce mutations and so on, it rarely if ever produces beneficial mutations and so on.

So yeah feel free to respond and we’ll move things on in the conversation.

Transposition, Epigenetics and Horizontal Gene Transfer are not magic incantations that explain things. They are well-documented, non-controversial systems that organisms use to change their DNA. These systems operate in everyday life.

The only magic incantation in this conversation is the word “random.” When anyone says an evolution event happened because of a “random mutation,” that statement is indistinguishable from magic and equally unscientific. This is because randomness is unprovable and the event cannot be reproduced.

In real life, systems never evolve randomly. Automobiles don’t, computers don’t, chemical plants don’t, and neither do fruit flies or cells. Randomness is just another word for “magic.” Transposition events are not random. Over 75,000 scientific papers show that they are highly structured and obey rules.

A scientist’s job is to discover patterns. Not deny them. PZ is advocating an anti scientific position… and then trying to shame me for explaining McClintock’s work to the public. Nothing about MClintock’s work was the discovery of “random processes.” In the conclusion of her Nobel Prize speech, she says:

“In addition to modifying gene action, these elements can restructure the genome at various levels, from small changes involving a few nucleotides, to gross modifications involving large segments of chromosomes, such as duplications, deficiencies, inversions, and other more complex reorganizations.”

So when PZ says “It’s hard to argue that there was a scheme or a plan behind them” he’s pretending 50 years of molecular biology never happened. The eminent scientist Lynne Margulis said in her book Acquiring Genomes:

“Many ways to induce mutations are known but none lead to new organisms. Mutation accumulation does not lead to new species or even to new organs or new tissues… Even professional evolutionary biologists are hard put to find mutations, experimentally induced or spontaneous, that lead in a positive way to evolutionary change.”

 

PZ: So what’s frustrating about talking to Perry here is he keeps throwing out these words as if they’re magic incantations that explain things.

So for instance when he was talking about my zebrafish and how they get better at living in a laboratory environment over years. He says ‘transposition’ and I’m sitting here wondering what the heck is he talking about.

Transposition is a very specific genetic and molecular phenomenon. You don’t simply say “transposition” as if solves everything because it doesn’t.

Transposition is another mechanism that causes random mutations in the genome. So in a sense he’s right yeah we get random variations in individual zebrafish that are then selected for by their presence in the lab environment that leaves the next generation, the survivors, being better able to live in a lab environment.

But as far as directedness, there’s absolutely no evidence for that. There have been many experiments done with transposons and flies and other organisms.

They do have specific sequences they like to zoom in on, but those sequences are common throughout the genome. So you can’t simply say that there’s some kind of directedness. There’s no purpose.

In fact the whole argument rests on the fact that he is proposing this amazing mechanism in which there is purposeful modification of the cell by the cell, and he’s the one with no evidence for that.

We’ve got decades worth of evidence in biology supporting the idea of random genetic change.

Perry: PZ, none of your evidence supports random genetic change because there’s no way to prove randomness in mathematics.

Now what we can do is we can say ‘does this fit certain patterns’ and you said it tends to conform to specific sequences. You know transposons don’t just jump to anywhere. There are certain places that they are more likely to go to than others. There is a definite pattern.

It’s kind of like if you read the newspaper the letter E is going to appear 13% of the time and the letter Z is going to appear about 0.1% of the time.

And we see a similar statistical profile in genetics where you see specific gene sequences specific percentages of the time, and if it was actually random you would not get these–they’re called, ergodic patterns–which is, for example the letter U almost always follows the letter Q in the English language.

That’s an ergodic pattern. There are ergodic patterns all over biology and they specifically and directly contradict your claims of randomness.

 

There is no way to prove that any specific sequence of symbols is random. I’m not ignoring the evidence; PZ is.

Darwinists assume random mutations cause evolution. This is impossible to prove. There is no evidence this is true.

Fact Check: “Code” in biology is not a metaphor. “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)

 

Host: You’re groaning, PZ. Why are you groaning?

PZ: Because he’s ignoring all the evidence. Yeah you’ve got a metaphor and you are shackled to this metaphor of a computer code or a language or whatever. It’s invalid here.

That when we do real biological experiments we can make predications about the results based on chance. And they work, they actually work.

So for example a really simple kind of experiment that I do with students every year is we are doing mapping experiments. We’re mapping genes in the genome. This is a process in which you encourage recombination. You do breeding experiments, and you get random recombination of pieces of chromosomes, and what that means if two genes are really close together there’s a low chance there will be a recombination event between them.

Fact Check: PZ’s example of homologous recombination is also a non-random process (it requires DNA sequence complementarity) and is subject to control by the cell. See for example:

Brick, K., F. Smagulova, et al. (2012). “Genetic recombination is directed away from functional genomic elements in mice.” Nature 485(7400): 642-645.

 

 

If two genes are far apart there’s a greater chance that there will be a recombination event between them. Just because of the physical properties of the chromosome. We can do this and what we see is that it works. That every time we can do mapping of genes, we can tell which genes are closer to other genes by looking at recombination frequency.

So this is a case where we’re using the predications of chance events in the genome to map out the structures there. Furthermore, when these same animals, these same organisms, are taken and subjected to a molecular gnome analysis, for instance we sequence the entire DNA strand what we find is that proportionally we’re largely correct.

Yeah that chance events do a really good job of mapping out the distribution location of genes on a chromosome.

Perry: But the breakage points are not random. You’re moving genes around, and the genes are staying intact or sections of the genes are staying in tact, they’re not just breaking anywhere.

When PZ says, “let’s not confuse this with a uniform random distribution… there are places that are hot spots for breakage” he’s just contradicted himself. A “hot spot” is a place where mutations happen more frequently. That by definition is non-random!

To a Darwinist, anything we don’t understand gets swept under a big giant rug called “randomness” or else “natural selection.” It’s abdication. PZ is just moving the operation of randomness from one level to another.

 

 

 

 

 

 

PZ: No they can… let’s not confuse this with a uniform random distribution. It’s not a uniform random distribution. There are places that are hot spots for breakage.

But when you look at this, yes, you do get cases where it breaks in the middle of a gene, and you get a recombination event that bridges right at the point of a gene.

You get them in the energetic region, but those are larger so you’re more likely to get them there.

Uh, that’s the point of the experiment is that when genes are far apart you get many more recombination events between them…

Host: Now, as a layman, coming in here between two people who obviously disagree, and I’m not following every aspect of this debate, but if I could try to boil it down as I often try to…

You’re saying on the one hand, PZ, when you get these events going on in the cell, at the genetic level, when you look at what’s happening when a cell’s repairing itself or whatever it’s doing, it’s doing it on the basis of statistical probabilities, will play their part.

Something will happen, but you can see that it’s happening because of the physics of the thing, and the way it all plays out.

Perry’s contention, on the other hand, is that no there’s something really purposive going on here that, in some way, the cell itself is exhibiting almost a desire let’s say to repair itself, rather than it just being the random events that, when all added together, do create something that ultimately helps the next generation to improve and all the rest of it. I’ve probably not described that brilliantly.

PZ: No, actually, I think that’s a good point to make. Yes, you would expect that if there was intent that this cell would be trying to optimize its condition, trying to select for, and without selection, just doing it by itself, designing and engineering a better solution.

But the thing is when we do those kinds of experiments what we’re typically comparing is deleterious and wild-type alleles. So we’ve got an allele that’s actually deleterious to the organism and we’re looking for a recombination event with a healthy allele.

And so what will happen is that by the distance separating them, they will sort out into some organism that will get two deleterious alleles, others will get a healthy one and a deleterious one and others will get two healthy alleles.

One prediction is if this was a purposeful event, you ought to get more with the double healthy combination, right? And what we find…

Host: So, it just looks like what you would exactly expect, from your point of view? 

PZ: Right, what we find is the distribution of the deleterious traits and the distribution of the healthy ones are dictated by chance, not by the well being of the poor fly that’s going to inherit them.

Host: Ok, what’s your response to that Perry?

Perry: There’s a video, it’s on the Evolution 2.0 Facebook page at the moment

where the University of Redding damaged a gene related to the tail of a bacterial flagellum. So the flagellum didn’t have a tail, and they came back after the weekend and the organism had repaired some gene and now had a tail.

Now, we see this over and over and over again when we look at genetic repair. That the cell is constantly trying to maintain the integrity of the genome, and, again, the latest Nobel Prize is specifically about the error correction. There are three layers of error detection and correction. The cell is militantly defending itself again random errors.

To give an analogy that listeners would understand – PZ, please tell me if I’m misquoting you – is suggesting that if this were a newspaper article, the words and phrases could get broken up in all kinds of unspecific, statistically random places and rearranged, and sometimes they’re helpful.

I’m saying they’re actually obeying the rules of a grammar, and the words are moving around intact, or subsets of words like words with two parts.

 

 

Host: There’s an editor somewhere in the background making sure that you don’t just end up with a scrambled article in some way. I’d like to move this to the bigger picture, because I’m obviously not going to get you guys to agree on these specifics about these genomes and so on.

One thing you make the suggestion of in the book is the Junk DNA debate that’s been going on for the last few years. You believe this is an example of the way in which your thesis is being born out in some way.

Perry: Yes. Craig Venter was asked not too long ago: “What is your opinion about junk DNA?” And he said a lot of arrogant people have prematurely announced that 90% of our DNA is junk, and he’s not willing to jump to that hasty conclusion. I think that’s a very hasty conclusion.

Nature is not nearly that wasteful. PZ says a lot of interesting things about junk DNA. He says ‘junk gibberish with occasional bits of translated code that convert to proteins with regulatory elements’.

PZ, your view of the genome as this kind of junkyard – I think it’s completely wrong. I think time will prove that wrong. I think it’s an anti-scientific position to take.

Host: Hmmm, throwing down the gauntlet there. PZ, explain briefly what junk DNA is, and why you think it is a good indicator of why evolution is, in that sense, a random process…

PZ: Well, yeah junk DNA–it’s a complicated term. There’s lots of things that are called junk DNA that are not junk DNA.

But roughly 90% of the human genome has no purpose along the lines of assisting us in our life, ok it has no functional role, no functional human role, although it may it have some selfish genome roles to play.

I have to throw the gauntlet back because, yes, I read Perry’s section on junk DNA. It was disgracefully dishonest. This is simply awful what he says here. I’ll just quote it from page 273:

It says:

…ENCODE’s finding were unambiguous. At least 80% of our DNA is active and necessary. If you deleted it, our bodies would fail. Our children or grandchildren would be missing something critical that they need to survive.

RETRACTION: PZ is right. Encode’s findings were not nearly as strong as my statement in the Evolution 2.0 book. My statement was misleading so I retract it.

“At least 80% of our DNA is active and necessary. If you deleted it, our bodies would fail” was MY opinion and not ENCODE’s findings.

I still predict that this is true, even though ENCODE’s findings don’t yet support it. ENCODE has found that over 80% of the genome is transcribed in a tissue-specific manner. 

I estimate at least 80% of our DNA is active and necessary. I believe it would take 100+ years of experiments with real humans to reach a definitive answer.

Do you know a pregnant couple who is willing to delete 80% of their child’s “Junk DNA”? If so, let us know.

One thing we do know about the non-coding regions of DNA is they contain sections of retroviruses.

In mammalian placentas there is a membrane one cell thick called the syncytium. It mediates transfer of waste and nutrients between mother and child.

Genome research indicates that the instructions to build the syncytium first came from code in the envelope gene of the HERV-W human endogenous retrovirus.

Also, so far as we can tell, different versions of the syncytium were constructed in mammals three different times from entirely different viruses. (Reference: Virolution by Frank Ryan.)

 

PZ: That’s a complete lie. I will say that right up front. Not even ENCODE, and I have a lot of disagreements with ENCODE, I don’t think they did a good job, but not even ENCODE would agree with that. That’s simply not something that they determined at all.

At the ENCODE experiments, they defined function as simply binding any other protein in the cell. It’s the loosest possible definition of function. They have done no experiments to determine whether those elements are active or necessary. And they definitely have not done any experiments in which they have deleted some of the junk DNA to see if it has an effect.

So to make that claim, this is very characteristic of his book, is that he makes this sweeping, strange arguments that are informed more by his prejudices than they are by actually evaluating the facts appropriately.

Another thing he says “the burden of proof that junk DNA is truly junk is on them until they understand everything and explain every nuance of the genome’s operation in precise detail until they can build a cell from scratch. Their job is not done.”

That is also false because most of the junk DNA we actually know what it does. For instance there are transposes that are part of the junk DNA that have no function for the cell. There are reverse transcriptases that are relics of past viral infections.

A lot of the junk DNA we have categorized, we know exactly what it does and it does not contribute to the well being of the organism.

Host: It’s kind of historic, hence the name Junk DNA that played a role at one point in our evolutionary history but no longer does, and, for you, is yet another reason to show why this – why the idea and purpose of this is –

PZ: Well, yes, and we actually know what it does. You know if you find a sequence – there are sequences called LINES or transcriptases, and we know exactly what they are, we know what their enzyme does. It copies RNA back into DNA, which is not a function that our bodies use, but viruses do.

Host: Let’s allow Perry to pick up this gauntlet again in order to throw it back across the line. [PZ: A little bit of gauntlet slapping.] Yeah absolutely, and I expected no less.

 

So far as I can find, the most DNA that has been deleted from a mouse with no discernible effect is 1-3%. Do you think extrapolating a 1 to 3% experiment to “90% junk” might be a bit of a reach? I welcome anyone with a better Junk DNA deletion example than the mouse experiment. Did it have “absolutely no effect?” The article says:

“Knowles cautions that the study doesn’t prove that non-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she says. “We don’t know if they have abnormalities that we don’t test for.”

“David Haussler of the University of California, Santa Cruz, who has investigated why genetic regions are conserved, says that Rubin’s study gives no hint that the deleted DNA has a function. But he also believes that non-coding regions may have an effect too subtle to be picked up in the tests to far.

“Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argues. “Darwinian selection is a tougher test.”

 

Perry: So, PZ, has anyone deleted this junk DNA and seen what you get?

PZ: Why, yes, there have been experiments where large structures of DNA have been deleted from organisms such as mice. And most of that has absolutely no effect. 

Perry: So I should predict that if you run the experiment 10 or 20 or 50 generations you will find that does get used. It is necessary, it is helpful and useful. I think it’s extremely premature to say that it’s junk. And if you can’t build an organism from scratch… 

Again, I go to what Craig Venter said, he engineered a synthetic genome, and injected into a cell, and got it to work. And if you did this on a grander scale, and you let the experiments run long enough, I think you would find there’s a whole bunch of stuff in there that’s not junk.

And one of the reasons I believe this is true, the human genome is only 750 megabytes; it’s about the size of a CD. Considering that 750 megabytes contains most of the instructions for building human, body yet Mac OS takes about seven CDs and Windows takes 20.

First of all I’m really impressed that the job gets done in 750. What you’re saying the job is actually being done in 75.

Which is just flat out extraordinary. I don’t think you can get that much good code in 75 megabytes. And if you can it’s the best code I’ve ever seen and so I think it’s really premature…

PZ might have a leg to stand on if bioinformatics was not such a successful discipline… or if DNA did not have so many strong parallels to computer information.

Excerpt from Evolution 2.0: DNA, like many human-made codes, also has redundancy (326), error correction (312), checksums (316), linguistic structure (403, 520), and codes layered inside of codes (675).

The nucleus of a cell stores data with a million times the density of our best hard drives. The genome stores an incredible amount of functional information into a very tiny amount of space.

So I predict that the 90% of DNA we don’t yet understand is not junk. The amount of so-called “Junk DNA” will fall every year until the term is abandoned entirely.

20 years from now, nobody is going to be defending the Junk DNA theory anymore.

About Metaphors: “DNA is a lot like software” is a metaphor. “DNA is code” is not a metaphor, because DNA by definition contains the genetic code.

trans_tcip_sTake a look at this visual comparison between transposons in DNA and the structure of data in Ethernet (click to open in a new window):

 

 

 

 

 

PZ: You don’t see that this metaphor is totally self-defeating? You’re trying to compare the human genome to information in code on a CD, and you’re pointing out that it’s really really tiny. Even if we count all the junk DNA as functional it’s still really really tiny.

Doesn’t that tell you right there that maybe you’re making an inappropriate comparison, that you’re dead wrong on trying to shoehorn the information in a cell into your rather naïve conception of digital information from an electrical information from an electrical engineer’s standpoint?

Perry: Well I don’t think that all of the information for building a human body is in the genome. I think it does reside in other places in the cell. But it’s a remarkably small instruction set that builds a remarkably sophisticated machine. Again we’re using metaphors.

Host: PZ’s fundamental objection though is that you’re using—you’ve come at this as an electrical engineer, a software engineer, so you’re seeing the biological processes with that set of filters and PZ says it’s not the same discipline—you’ve got the wrong analogy.

I’m interested to hear from you, Perry, why you think this is an absolutely valid analogy for biological systems.

Perry: Well, two reasons, Craig Venter, is not just a software engineer, he’s a biology engineer, and he’s very good at it. And he says this is premature, and he’s got a lot of credibility with me.

And secondly it’s because bioinformatics is such a rapidly advancing field, as is Systems Biology, that when somebody violates a basic mathematical principle—mainly information entropy, and I know that in all of the other analogous systems, what he’s saying would never work—then I question his model.

All I’m saying is what’s going on here is non-random, and the non-random hypothesis is more consistent with the spirit of science than the randomness.

Because as soon as you say ‘random’ inquiry stops, then there’s not further dissecting what’s going on. There’s a pattern here.

Host: PZ? 

This is not about Electrical Engineering or even software. This is about the fact that the math (“random” is a mathematical term after all) doesn’t work. And if the math doesn’t work, it’s a bad theory. No matter what. If you’re going to build a scientific model of anything, the math has to work.

Good-old-boys clubs always get offended when outsiders show up and raise the game. The taxi companies are very upset about Uber. But customers like Uber because taxis give them a lousy, over-priced experience and Uber gives them an affordable, pleasant experience.

 

PZ: Yeah I would love to hear Perry question his own model because he’s not doing that. Over and over again what you do is you tell me ‘well from my perspective as an electrical engineer this doesn’t work, it can’t work’ and I’m telling you yeah but biology does work, so maybe your perspective is wrong.

Maybe you’re coming at this from an invalid angle. Yet you just come back and insist on applying these fallacious ideas about electrical engineering to biology. It’s like we’re in a constant circle here where you refuse to consider the possibility that you’re wrong.

I also have to point out one other thing and that is every time I get in an argument with a creationist they fall back on this appeal to authority. Craig Venter is a smart guy, and he’s really good at what he does, but he’s not an evolutionary biologist in any sense of the word.

In engineering, the standard for claiming you understand something is: You can build it, and it works. Venter builds stuff that works. I won’t believe anybody’s Junk DNA hypothesis until they can demonstrate experimentally that the Junk DNA really is unnecessary.

I find an astounding lack of curiosity about how things actually work among Darwinists. They are too often content with hand-waving explanations that have no substance.

I also find the same tendency among creationists. If natural processes can bring about evolutionary events, wouldn’t you want to know about it?

 

He does not do evolution. He does brute force molecular biology. And so to argue that because Craig Venter is unfamiliar with the evolutionary arguments against his interpretation does not hold any water with me at all.

Perry: It’s the brute force molecular biology that I respect. Because he has to build a functional cell, and he doesn’t really concern himself with where it came from.

Your junk DNA theory comes from where you think it came from, or how you think it got there, and I believe you’re wrong. And the proof is in the pudding.

If you can build a successful cell then you must know something about the genomics. And I think he knows. 

[break]

 

 

Host: As we come back from break…

Perry, you’re a bit of a person who likes to throw challenges and gauntlets as we’ve already experienced in the program.

One of the things you’ve offered is a prize for someone who can solve this riddle in a naturalistic way. Do you just want to explain what this Evolution 2.0 Prize is?

Perry: Yes, the genetic code is one of those central discoveries of all modern science, and when I began to understand: encoding, decoding, copying, all of that, everything began to make sense.

And what I observed was that all of the other codes that we know the origin of are designed.

We of course don’t know where DNA came from, and we don’t know of any codes that aren’t designed that fit the definition of a code.

So early on I was going around and I thought ‘I’ve got a really awesome God of the gaps argument.’

But I shifted my position, because I got in this discussion with my brother and he’s like “So, Perry, what do you expect scientists to do? Say ‘OK, God did it’ and then go out to lunch? I mean come on.”

He had a point! When you shift from ideological concerns to doing the practical work of science… you know that all science can do is peel the onion another layer and another layer and another layer. 

Maybe this is solvable. And we should understand where codes and where information come from.

I heard Richard Dawkins say the origin of life was a ‘happy chemical accident’ and I was appalled at what an unscientific answer that was. And so I decided to put together a technology prize.

So with a considerable effort, forming a company, forming a private equity investment group, right now were offering 3 million dollars if someone can produce a patentable process that generates codes without cheating. And I think this would be a very valuable thing to achieve.

Host: And would that effectively disprove at some level your view that the cell is doing it itself or what would be the purpose, I suppose.

Perry: I think it might tell us something about deeper principles in the universe that what we haven’t yet discovered, that might explain a lot about what goes on in biology. Biological organisms are really amazing I’m sure Mr. Myers would agree with that, they are amazing. And I think there are some bigger pieces of mystery that we are missing.

The investors who are backing the Evolution 2.0 prize are serious. If this problem is solvable, then they want it solved, and they want to own the patent. If somebody solves this, they’ll get a LOT more recognition than just money. This will be one of the ten most important science discoveries of the 21st century. And yes, they’ll get the money

 

Host: What do you think about Perry’s prize, PZ?

PZ: Oh, I think it’s a sham.

Host: You’re not going to put your hat in the ring, and try and win this 3 million dollars?

PZ: No, because there’s no way he’s going to give the prize to anybody.

This is exhibit “A” of “begging the question: Assuming the very thing you’re supposed to prove… then offering it as proof.

Maybe the origin of DNA is a miracle. Or maybe it’s purely natural. But we can’t be sure it’s natural because there’s not yet any proof for how it got here.

PZ, where is your proof that it “spontaneously emerged”? How is this a scientific theory?

 

 

If I were to say OK I’ve got one for you it’s called DNA and genetics and biology. There is no designer behind it. It’s a code that spontaneously emerged and has evolved over 3 billion years–he’s not going to accept it, he’s going to say it’s not going to count.

Host: Well, I guess that’s what he’s saying—this is precisely a code which, in every other instance where we have a code of similar kind, we know it’s been designed, engineered and so on; why would we assume that this is the only counter example to that—I suppose is Perry’s point.

PZ: Well, one good reason is that the code evolved when there were no humans around. Humans are really good at generating codes and signaling and all that kind of stuff. But this is a case where we weren’t around 3 billion years ago, so we’re off the hook on that one.

But I would say the bias goes the other way. Perry has said specifically that all codes are created by a conscious mind. This is not demonstrated, this has not been shown.

What’s far more interesting is that naturalistic processes can generate something as complex as a cell. So just to assert that all codes are created by a conscious mind…

Host: Is that an assertion on your part Perry?

Perry: It’s a misquotation. All codes we know the origin of are designed.

And, PZ, you said it spontaneously emerged. Could you please give us evidence through a repeatable scientific process that confirms your assertion?

PZ: First of all let me just say that was not a misquote. It’s on page 192 of your book where you say “all codes are created by a conscious mind, there is no natural process known to science that creates coded information.” 

Perry: That was the way I originally stated it in 2005. And then you’ll see as you turn the page that I updated it a little bit to my current stance.

PZ: Which is no difference from your original stance.

Perry: …that all codes that we know the origin of are designed.

PZ: Ok, let’s get back to your original question—how do we know that these are a product of natural processes? It’s because we’ve got historical information, so we can’t repeat history of course, if would be nice if we could, but we can’t. 

But we’ve got historical information about when these code originated, and it was at a time when the earth was an oxygen-free hell, and so there weren’t our kinds of intelligences around at that time. It also rose entirely in single celled organisms.

So unless you’re going to argue that those single celled organisms were intelligent, that shows that no it had to be a natural process that generated them.

Perry: So you’re assuming that it was a natural process, but you can’t reproduce the event. And we don’t know that much about it.

PZ: Can you? Are you going to simply assert that it was magic? Or that it was a god who appeared or whatever that just did it with the wave of his wand?

Perry: I’m trying to get away from magic, which is why I’m offering a prize for somebody that can actually produce an experiment. Rather than make an assertion.

Host: We’ve gotten to the God question, which I did want to get to eventually, because what are you saying I suppose, Perry?

If you’re right and PZ is wrong let’s say, and that really there is this extraordinary ability in cells that most of science has not woken up to, the fact of that means it’s not random, that there’s this kind of purposive directiveness to the way that organisms change over time that’s built in from the first seed I suppose, the first DNA molecule that appeared — it was all there ready to roll.

Are you saying we can only actually at present explain that as the product of a conscious mind? And by that we’re probably going to be talking about something a bit like God I suppose. 

Perry: Currently that would be the inference. But I am reluctant to make God of the gaps arguments and pronouncements. 

What I would really like to see is somebody to make real progress on this issue. Because my theological views don’t hinge on God magically creating a cell.

Maybe there is a principle that we have not discovered, that gets you from matter to information and to cells. And if that exists, we sure should find out what it is. And if it’s a scientific theory, it’s repeatable, it’s based on principles.

PZ is not giving us any principles. He’s asking for a free diplomatic pass of immunity, if you will. And I’m saying really there’s very little we know about origin of life that currently qualifies as science. And let’s improve that. That is what I’m saying.

I don’t believe in pitting theology against science. I’ll tell you what I’ll ask for a diplomatic pass of immunity is: I believe God created a universe that is orderly and structured and discoverable and directional; and all the rest is discoverable because evolution makes the universe an open book.

So my bias is to believe that we can uncover the mysteries, but there is, at minimum, a principle that’s being ignored here.

And I’m very serious about finding it. This is not a joke.

Host: Alright, what do you have to say to that, PZ? 

PZ: Well, a couple things. I would recommend that he read Princeton’s Nick Lane’s recent books on the subject. Currently what a lot of people are pursuing is this metabolism first model of the origin of life where it’s not a matter of code, it’s a matter of chemistry.

And that seems to be really successful. I would also point out that we do have a lot of information about the origin of these things. There have been a number of studies for instance where we do comparative genomics, and we ask ‘ok what’s in common with every creature on earth’, and we can thereby work back and figure out what the early gene set was.

And doing that we can determine something very specific about what genes were present in early organisms, what kind of environment they lived in, what kinds of chemistry they had to do to survive.

What we see is again a pattern of common decent derived from these ancestral organisms that implies, of course it doesn’t prove, but it implies that if we keep going back we’ll get simpler and simpler, and we can figure out what those early organisms were.

And that is a productive scientific approach rather than saying ‘it can’t happen, that all codes are created by a conscious mind therefore there was no natural process that could generate those’. 

If we’re scientists, we’re looking for natural processes, that’s what real scientists are doing.

We’re not sitting around writing books based on electrical engineering to impose their views on a discipline totally inappropriate to that perspective.

Host: So, I don’t think you’re going to get a good review from PZ on Amazon, Perry, but if someone is teetering on the edge of getting hold of your book, what reason could you give them to pick it up?

Jerry Coyne’s and Richard Dawkins’ books give good anecdotal evidence for evolution itself. They teach you nearly nothing about how it works.

Much of what they do say about how evolution works is awful. They largely omit and downplay epigenetics, transposition, symbiogenesis etc.

They offer very little in terms of real-time evolution experiments. They are peddling a model that is 30+ years out of date.

Bill Nye’s book is very nicely written but it’s essentially for sixth graders. It’s just as outdated as Coynes’ and Dawkins’. The evolution book by “the science guy” contains almost no science education at all.

I’m surprised because Bill Nye is a mechanical engineer. I expect better work from an engineer. Engineers tend to like Evolution 2.0. It’s often the first explanation of evolution they’ve heard that makes sense.

 

Perry: When I started reading evolution books, I was… ‘disappointed’ would be a mild word… at the lack of rigor that I found in popular books by Richard Dawkins, Bill Nye, Jerry Coyne, people like that.

They told you very little of any real substance about how the evolutionary process happens.

They told you what happened, but they didn’t tell you how. As I went down the rabbit hole and discovered things like horizontal gene transfer and symbiogenesis, I found this extraordinary experimental evolution which many people were strangely silent about, and this tells that story.

I said: This story needs to be told! People can come to philosophical conclusions on their own. But they at least need to know what these experiments achieved.

Host: I’m glad for PZ taking up the challenge, at the very least, to come and debate it with you. Because I think there’s loads of people who simply wouldn’t take that up in the first place. But thank you, PZ, for being on the line to us. If you want to find out more about PZ – pharyngula.com or look him up on Google. Same for Perry: http://www.Cosmicfingerprints.com/evolution for more on Evolution 2.0.

Please post your comments and questions below. All comments must be civil and include your REAL first name and last name. All others will be deleted.

211 Responses

  1. Wendell Read says:

    Perry, You did a marvelous job of getting across the fact that the basic principles and laws regarding communication theory have to be respected by biology. Biology does not get a free pass.

    • Thank you Wendell. Spread the word and share!

      • EHMAI justin says:

        I have the code that will prove you both wrong and right at the same time. lend an ear to understand?

      • Brian Platt says:

        Is it really “bliss” as the saying goes, Perry? Being beaten down by your intellectual betters must be a very humbling experience.

      • bruce says:

        I think you make the mistake of allowing the evolutions/atheists the hallowed ground of objectivity. they are in fact demonstrably biased. they are atheists who put on labs coats and peddle their religion as science. Evolution is the creation myth of the atheist. Accept that and keep doing the real science.

    • Andy Holland says:

      Evolution means slow – what actually occurs is fast. Evolution implies pseudo random, what actually occurs is directed to ascent of intelligence.

      Being sole inventor of the self-verifying application resident compiler, and a textual n-recursive text algebra used in nuclear reactor design and automation, I know for a fact that writing self-verifying and correcting code is very possible in software space. It also requires a heck of allot of intelligence to use properly.

      The problem we ran into with automated design is one can construct a complex objective function on anything programmable. That leaves an infinite space for increasing complex objective functions. There is no such thing as a “simple” system at a certain juncture and the more smarts you put into something, the more you need to effectively use it. Beautiful design meets a huge number of competing objective constraints. The set that works well is very small compared to the possibilities.

      DNA has 3GB per strand. If one typed that out it would be over 1000 reams of paper, 2KB per side. To form at 4 bits per byte 2KB at random is one chance in 10 to the over 2000 power. And transposition requires more intelligence, more information to make a mechanism like that work. So where does such a sophisticated mechanism come from? Not random – random is weak without Logos – Word. “In the Beginning was the Word” – not a guy in a sheet, but God in essence un-depictable, eternal, who revealed Himself to us in the temple of a body.

      There is no such thing as junk DNA according to ENCODE data. The repairing properties are incredibly sophisticated. It came from somewhere or someone complex, eternal, non-compound, unoriginate – The Word.

      The ID guys are owed the greatest scientific apology in history. Organizational, energetic and informational entropy are real, and to overcome them requires massive intelligence in the Beginning. The atheists are truly fools – but God has given them a strong cup of delusion to drink, and they will drink it to the dregs before the good Lord reveals Himself, and all excuses disappear. He already has revealed Himself, and the sophists are proven delusional and are proven cruel. They wish to Lord over others, or act like unrestrained animals, and that drives the godless delusion along with arrogance.

      • Andy, thanks for your comments on recursive code. Reminds me of STUXNET which was a major accomplishment by somebody. Tell us more if you’re able.

        Any relation to the late John Holland, famous for genetic algorithms?

      • Boyd musick says:

        You are so right! Every knee will bow and every tongue confess. Science will never solve what can’t be observed or created from nothing.

    • Raphael Wettenstein says:

      Hello Perry Marshal –

      With great interest and awe I watched your superbly articulated video discussion.
      It was not as much of the presentation that touched me, I was pleasantly surprised as you so clearly echoed what I`ve known for a long time.

      I`m now a certified hypnotist, and long time researcher of the unknown, as well as mysteries of life.
      From early childhood I was an artist who evolved into having a career as commercial artist, ( my first love ).

      Being a nature lover, including the human anatomy, I am always contemplating how the designer`s ideas are coded and expressed in there is.

      As a second occupation I became a certified hypnotist, as I am long time researcher of the unknown, as well as mysteries of life.

      I would like to share with your readers my painting, DNA OF CREATION (2013), which, according to Jewish Kabbalah, an artistically interpretation of my understanding, and it reflects yours as well.
      Question – How to post my painting, since I don`t have a website?

    • John Moore says:

      Perry:

      I just finished Evolution 2.0. I clapped out loud at the end. Thanks!

      Help me to understand what PZ is saying about McClintock’s work. As I recall from the book, McClintock irradiated maize (‘what you call, “corn”‘…couldn’t resist). The radiation damaged the chromosome…perhaps even at “random” places. As I came to understand McClintock’s from your book, transposition took place to repair the “random” breaks to restore the function of the cell. What is “random” about the repair?

  2. Excerpt: “Contrary to what PZ said, McClintock’s work is explicitly about cells engineering solutions! That is her point.”

    Thanks to Perry Marshall for bringing this to the attention of others. In the interview he shows how futile it is to attempt discussion of biological facts with those who are biologically uninformed.

    PZ Myers, for example, ignores everything known to serious scientists about the nutrient-dependent innate immune system, cell type stability, and the stability of organized genomes.

    That nutrient-dependent stability is maintained across species via the physiology of reproduction.

    The nutrient-dependent physiology of reproduction links what organisms eat from RNA-mediated events to chromosomal rearrangements.

    The systems complexity of the epigenetically-effected chromosomal rearrangements links everything known about physics, chemistry, and the design of the conserved molecular mechanisms of cell type differentiation. The only need to mention mutations is to place them into the context of all virus-driven pathology.

    When people like PZ Myers attempt to debate biological facts and to put mutations into the context of their neo-Darwinian nonsense about evolution, they always lose. The dialog between Marshall and Myers adds another epic loss to the neo-Darwinian army.

    Marshall’s accurate representations of biologically-based cause and effect encourage others who are interested in “Combating Evolution to Fight Disease.” No biologically informed researchers are combating the representations in Evolution 2.0; all of them are dismissing mutation-driven evolution. Perry Marshall’s book will help you to dismiss the nonsense touted by PZ Myers and others.

    See also: http://tinyurl.com/hssspmy

  3. This may be of interest: In The Beginning Was Information, A Scientist Explains the Incredible Design in Nature by Dr. Werner Gitt (Free Videos, Free Books, Free MP3s) http://www.puritandownloads.com/in-the-beginning-was-information-a-scientist-explains-the-incredible-design-in-nature-by-dr-werner-gitt-free-videos-free-books-free-mp3s/

  4. Charles Baehman says:

    Is photosynthesis a intelligent or designed pattern?

    • It is a very, very, very sophisticated system which is possible only because of chloroplasts (which are actually blue-green algae in symbiotic relationship with eukaryotic plant cells) turning sunlight into energy. Which requires DNA and code to exist first.

      • See also: Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production
        http://tinyurl.com/jog998w

        It is a technical representation of what is required to design photosensitization in a nonphotosynthetic bacteria. Cysteine is the amino acid substitution that stabilizes the hydrogen bond energy.

        It links their design from the innate immune system to DNA repair. Nutrient-dependent amino acid-dependent DNA repair prevents virus-driven entropy of organized genomes.

      • Brett says:

        It’s also believed to be/involve a quantum mechanical process from what I’ve read about it. Pretty Fascinating.

        • Jonathan Pinchbeck says:

          Everything in the physical world is ruled by a quantum mechanical process of some kind or another (Heisenburg’s uncertainty principle, di-pole bonding, entanglement, quantized energy states…etc). Stating so is redundant.

  5. Have you seen this information:

    “The earth’s magnetic field is not only a good navigational aid and a shield from space particles, it is powerful evidence against evolution and billions of years. The clear decay pattern shows the earth could not be older than about 10,000 years.” – The earth’s magnetic field: evidence that the earth is young by Dr. Jonathan Sarfati http://creation.com/the-earths-magnetic-field-evidence-that-the-earth-is-young

    Mercury’s Magnetic Field is Young! by D. Russell Humphreys http://creation.com/mercurys-magnetic-field-is-young
    Once again, a NASA space probe is supporting the 6,000-year biblical age of the solar system. On 14 January 2008, the Messenger spacecraft flew by the innermost planet of the solar system, Mercury. It was the first of several close encounters before Messenger finally settles into a steady orbit around Mercury in 2011.1 As it passed, it made quick measurements of Mercury’s magnetic field and transmitted them successfully back to Earth. On 4 July 2008, the Messenger team reported the magnetic results from the first flyby.2 As I mentioned on the CMI website earlier,3,4 I have been eagerly awaiting the results, because in 1984 I made scientific predictions—based on Scripture—about the magnetic fields of a number of planets, including that of Mercury.5 Spacecraft measurements 6,7 have validated three of the predictions, highlighted in red in the web version of the 1984 article. READ MORE AT http://creation.com/mercurys-magnetic-field-is-young

    “A separate article in the Journal about recent moon discoveries by physicist D. Russell Humphreys3 reported findings published by Clément Suavet et al. in the Proceedings of the National Academy of Sciences.4 Humphreys explained how measurements of magnetization of lava from a basalt ‘sea’ of the moon conflict with models of how the magnetic field works. “The report shows that uniformitarian scientists, because they assume the world is billions of years old, are still very puzzled about the moon’s magnetic field,” Humphreys said. “They don’t understand why it was formerly strong but now doesn’t exist, or how it could exist in the first place.”

    “On the other hand, the moon’s magnetic data fit creation science theories very well. A Bible-based theory for how God created the initial magnetic fields of planets and moons gives a created (6,000 years ago) field for the moon that is about as strong as the earth’s field is today, in accord with the measurements in the latest moon samples.” These latest findings from the moon are reported in the latestJournal of Creation along with much other creationist research. – Moon formation theories way off orbit by Tas Walker at http://creation.com/moon-formation-theories-fail

    • Reg,

      Thanks for stopping by.

      I have not studied the specifics of these particular items you bring up.

      What I can say is that I have Starlight and Time by Dr. Humphries and it is a poor piece of scholarship. My background is electrical engineering and the speed of light poses sever problems for YEC. If the speed of light is changing, most of physics (which for the most part works beautifully) immediately unravels because the speed of light is central to many calculations. The fact is, physics as it is with speed of light constant works supremely well. I am not aware that Humphries adequately addresses this.

      If Humphries’ work in these other fields is similar to Starlight and Time, I don’t find him very credible. I expect to easily find interpretations of the magnetic field data that support an old universe if I go looking. Physicists, geologists and even oil men who embrace a young earth are few and far between.

      I have Safarti’s “Refuting Compromise” and my read is that he’s married to a very specific theological interpretation and forces the scientific data to fit it. So I’m not very sympathetic to the young earth view.

      I do hope you find some things here that prove to be useful in your conversations with skeptics. When I give talks to YEC groups, I consistently have people who, at the end, become FANS of evolution, rather than being afraid of it. And that surprises the skeptics.

      • Thanks for the response Perry, though we clearly disagree. Do you realize that if evolution is true the Bible is not the Word of God, and they is no good news of salvation in Christ? Here is one reason why, though there are many: “The idea of millions of years came from the belief that the fossil record was built up over a long time. As soon as people allow for millions of years, they allow for the fossil record to be millions of years old. This creates an insurmountable problem regarding the gospel. The fossil record consists of the death of billions of creatures. In fact, it is a record of death, disease, suffering, cruelty, and brutality. It is a very ugly record. The Bible is adamant though, that death, disease, and suffering came into the world as a result of sin. God instituted death and bloodshed because of sin so man could be redeemed. As soon as Christians allow for death, suffering, and disease before sin, then the whole foundations of the message of the Cross and the Atonement have been destroyed. The doctrine of original sin, then, is totally undermined. If there were death, disease, and suffering before Adam rebelled-then what did sin do to the world? What does Paul mean in Romans 8 when he says the whole of creation groans in pain because of the Curse? How can all things be restored in the future to no more death and suffering, unless the beginning was also free of death and suffering? The whole message of the gospel falls apart if one allows millions of years for the creation of the world.” – The Necessity for Believing in Six Literal Days by Ken Ham at http://tinyurl.com/6gw4r9p. Also hear Six Day Creation & The Eisegesis Problem by Ken Ham (Free MP3) at http://tinyurl.com/jxfuwmv and “The Doctrine Of Original Sin (26 Free MP3s) by Jonathan Edwards at http://tinyurl.com/gvzvu2l.

        • “Do you realize that if evolution is true the Bible is not the Word of God”

          That belief is the problem.

          The Bible never teaches that there was no physical death – no animal death before the fall.

          Where does it ever say that? Show me.

          Adam and eve ate fruit, did they not? How do you eat fruit without killing cells?

          Did they never ever step on a bug?

          Did sharks have no use for those teeth, and they just ate vegetables?

          These are real problems for YEC.

          Did no lion ever kill a rabbit? Where would you ever support such a notion from scripture?

          This is bad theology.

          Death here is spiritual death, not physical death. It’s loss of fellowship from God. Now, if they had retained that fellowship immortality of men MAY have been possible – at the very least through healing of disease through the power of God.

          Notice that when Adam and Eve ate the fruit, in the day that they ate of it they did surely die. But not physically.

          True?

          Again this is bad theology and it FORCES you to accept bad science at the same time. YEC is the worst of both worlds. My brother went from missionary and seminary grad (Master’s Seminary, John MacArthur’s school) to nearly atheist partly because he figured out… there is no way yec is true! You have to band-aid the thing together with all kinds of bad science. And you have to guilt and fear people into not examining the science.

          When Paul says creation groans because of the curse, it’s because man lost his ability to steward the earth, and began abusing it instead. Creation longs for a caretaker who is not corrupt and struggling with sin and addictions. Who knows how earth would flourish if man’s connection to God was fully restored?

          This does not create any problem for the gospel at all. The Bible is not adamant that death, disease, and suffering came into the world as a result of sin. Where does it say that?

          Ken Ham said that. Scripture never said that.

          Ken Ham has piled a giant burden of legalism, guilt and fear on the world and it’s simply not true. He is piling assumptions on top of assumptions. Answers in Genesis is a tangle of LEGALISM, FEAR AND GUILT. And bullying tactics by Ken against Christian organizations who dare teach differently. I know the founder of a home school curriculum who was threatened by Ken – “I’ll smear your ministry publicly if you start teaching old earth.”

          I suggest the book “Historical Genesis” by Richard J Fischer. It will give a completely different perspective on the history of man which I find to fit science with the Biblical story much better.

          • I don’t want to seem unfair, but it’s clear you’re not very familiar with young-earth literature. The Bible never teaches there was no physical death? In Gn 1:29-30, God made it clear that man’s diet as well as animals’ would consist of seed-bearing plant and every tree that has fruit with seed in it. Besides, when God commanded to man that eating from the tree of the knowledge of good and evil “you will surely die” (2:17) makes no sense if physical death was already planned. The same is true for Gn 3:19. I could add that Acts 3:21 speaks of the restoration of everything. So if physical death was always present, does it mean that creation will be restored to billions of years of death and suffering? You may well say that Coyne criticized your book without reading it, but what’s the point if you criticize YEC’s position without considering its classics? For example, most of your questions have been answered both in “The Creation Answers Book” (Chapter 6: How did bad things come about?): http://tinyurl.com/j9mg7by and Jonathan Sarfati’s “Refuting Compromise”. In the latter, Sarfati especially answered Hugh Ross, a progressive creationist who made the same canards as you, by asking what about cell death and stepping on a bug. In page 205, he wrote: “Creationists have often pointed out that the creatures affected were those the Bible calls nephesh chayyah. When it refers to man, it is often translated by ‘living soul’, but, of other creatures, including fish, it is often translated ‘living creature’. However, it is never applied to plants or invertebrates. Therefore, there is a qualitative difference between the deaths of the vertebrate animals called nephesh chayyah and plant death. This is further supported by the account of the Flood and ark. The living creatures (nephesh chayyah) rescued on the ark did not include plants (or invertebrates)”. Insects aren’t considered nephesh chayyah in the Bible at all. It brings us now to cell death, Sarfati wrote (p. 210): “Cells are hardly nephesh chayyah. We humans shed millions of ‘dead’ skin cells all the time, but none of these were ever ‘living creatures’ in their own right”. He then extends the discussion on apoptosis (programmed cell death). So come on and do your homework!

            • Nowak,

              Which clarification of Romans 1 makes more sense – the first one or the second?

              12 Therefore, just as sin entered the world through one man, and physical death through sin, and in this way physical death came to all people, because all sinned—

              13 To be sure, sin was in the world before the law was given, but sin is not charged against anyone’s account where there is no law. 14 Nevertheless, physical death reigned from the time of Adam to the time of Moses, even over those who did not sin by breaking a command, as did Adam, who is a pattern of the one to come.

              15 But the gift is not like the trespass. For if the many physically died by the trespass of the one man, how much more did God’s grace and the gift that came by the grace of the one man, Jesus Christ, overflow to the many! 16 Nor can the gift of God be compared with the result of one man’s sin: The judgment followed one sin and brought condemnation, but the gift followed many trespasses and brought justification. 17 For if, by the trespass of the one man, physical death reigned through that one man, how much more will those who receive God’s abundant provision of grace and of the gift of righteousness reign in physical life through the one man, Jesus Christ!

              18 Consequently, just as one trespass resulted in condemnation for all people, so also one righteous act resulted in justification and physical life for all people.

              …..

              12 Therefore, just as sin entered the world through one man, and spiritual death through sin, and in this way spiritual death came to all people, because all sinned—

              13 To be sure, sin was in the world before the law was given, but sin is not charged against anyone’s account where there is no law. 14 Nevertheless, spiritual death reigned from the time of Adam to the time of Moses, even over those who did not sin by breaking a command, as did Adam, who is a pattern of the one to come.

              15 But the gift is not like the trespass. For if the many spiritually died by the trespass of the one man, how much more did God’s grace and the gift that came by the grace of the one man, Jesus Christ, overflow to the many! 16 Nor can the gift of God be compared with the result of one man’s sin: The judgment followed one sin and brought condemnation, but the gift followed many trespasses and brought justification. 17 For if, by the trespass of the one man, spiritual death reigned through that one man, how much more will those who receive God’s abundant provision of grace and of the gift of righteousness reign in eternal life through the one man, Jesus Christ!

              18 Consequently, just as one trespass resulted in condemnation for all people, so also one righteous act resulted in justification and eternal life for all people.

              …..

              Regarding plant vs. animal vs. human death – so no elephant ever stepped on a cat? What are the shark’s teeth for? What are the lion’s fangs for? Are they for eating vegetables?

              • John donnelly says:

                But since sharks, lions and many other creatures have sharp teeth, strong jaws and other features that were well designed for capturing and killing other creatures and other creatures have amazing defense structures and behaviors, doesn’t this prove that many creatures were carnivores right from the beginning? No, it is a demonstrable fact that creatures that are normally carnivores can survive on a vegetarian diet.9 Also, to change herbivores into carnivores God would not have needed to make changes to body parts. We know now that much of the genetic code that used to be called “junk DNA” has a regulatory role controlling the function of other genes. By His curse in Genesis 3, God could have simply “turned on some genetic switches” so that creatures’ behavior was changed.10 Using a computer metaphor, God didn’t have to change the hardware of creatures, but only turn on some of the software that He had built into the creatures at the beginning (but left in the “off” position) with the foreknowledge that man would sin and God would curse the creation.11 This is not a wild idea for it is implied by God’s judgment of Adam and Eve. Eve had increased pain in childbirth and the bodies of Adam and Eve began to suffer from processes that would eventually lead to death. Yet there is no reason to think that their body structures were significantly modified (or new body parts added) when God judged them”
                Just a quote from Mortensen in the article http://tinyurl.com/jl737za
                I think the problem is with the theistic evolutionist if one reads the whole article above . He even uses your IT analogy Perry .
                No,man caused the physical death and he is culpable . Hence the need for Christ as remedy . YEC allows the bible to speak for itself rather than secular science dictating the bible.

                • John donnelly says:

                  But since sharks, lions and many other creatures have sharp teeth, strong jaws and other features that were well designed for capturing and killing other creatures and other creatures have amazing defense structures and behaviors, doesn’t this prove that many creatures were carnivores right from the beginning? No, it is a demonstrable fact that creatures that are normally carnivores can survive on a vegetarian diet.9 Also, to change herbivores into carnivores God would not have needed to make changes to body parts. We know now that much of the genetic code that used to be called “junk DNA” has a regulatory role controlling the function of other genes. By His curse in Genesis 3, God could have simply “turned on some genetic switches” so that creatures’ behavior was changed.10 Using a computer metaphor, God didn’t have to change the hardware of creatures, but only turn on some of the software that He had built into the creatures at the beginning (but left in the “off” position) with the foreknowledge that man would sin and God would curse the creation.11 This is not a wild idea for it is implied by God’s judgment of Adam and Eve. Eve had increased pain in childbirth and the bodies of Adam and Eve began to suffer from processes that would eventually lead to death. Yet there is no reason to think that their body structures were significantly modified (or new body parts added) when God judged them”
                  Just a quote from Mortensen in the article
                  http://tinyurl.com/jl737za

                  I think the problem is with the theistic evolutionist if one reads the whole article above . He even uses your IT analogy Perry .
                  No,man caused the physical death and he is culpable . Hence the need for Christ as remedy . YEC allows the bible to speak for itself rather than secular science dictating the bible.

                  • This article assumes, but does not with scripture, that there was no death before the fall. The author imposes an arbitrary definition of good.

                    Romans 5 is about spiritual death not physical death, as I point out in an earlier comment on this thread.

                    Are there any known fossils of sharks or lions with vegetarian teeth?

                    • John donnelly says:

                      Perry
                      I’m glad you allowed my comment and it does show that you’re willing to engage with the YEC view .
                      The last sentence though is smart Alec like . Pandas have sharp teeth and they eat bamboo . Fossils of lions and sharks with sharp teeth do exist . They were vegetarian before the fall . The fall or sin caused the physical death .
                      We will have to agree to disagree , simple as . I believe your approach is a theistic evolutionist one . Nevertheless it is important for me and my ilk to come along side you to point out what I feel is good about your ministry and I enjoyed the debate above . Perhaps attack the presuppositions a little more and you will be even more successful in my opinion . Indeed one of the replies on here was superb as it approached this topic from a presuppositional standpoint and greatly undermined the opposing argument .

                    • I apologize for the snark.

                      Let’s start with something very concrete and basic: The speed of light.

                      If a galaxy is 100 million light years away, how long ago did the light leave the stars?

              • Jeffrey C. Long says:

                But….
                1Co 15:16  For if the dead rise not, then is not Christ raised: 
                1Co 15:17  And if Christ be not raised, your faith is vain; ye are yet in your sins. 
                1Co 15:18  Then they also which are fallen asleep in Christ are perished. 
                1Co 15:19  If in this life only we have hope in Christ, we are of all men most miserable. 
                1Co 15:20  But now is Christ risen from the dead, and become the firstfruits of them that slept. 
                1Co 15:21  For since by man came death, by man came also the resurrection of the dead. 
                1Co 15:22  For as in Adam all die, even so in Christ shall all be made alive. 
                1Co 15:23  But every man in his own order: Christ the firstfruits; afterward they that are Christ’s at his coming. 

          • Hugh says:

            ‘Death here is spiritual death, not physical death. It’s loss of fellowship from God. Now, if they had retained that fellowship immortality of men MAY have been possible – at the very least through healing of disease through the power of God.

            ‘Notice that when Adam and Eve ate the fruit, in the day that they ate of it they did surely die. But not physically.’
            No. we are made in God’s image: eternal spirit. Our spirit cannot die; the tragedy of eternal existence unredeemed, and without a new body, is Hell. Adam and Eve died physically within the first Day which was 1000 years in length. No-one lived longer than 1 Day; though Methusaleh came closest. All those who are raised up to reign with Christ (at his Second Coming) during the ‘Last Day’ will experience a full Day of life before the Last Judgment, etc.

            • And the Lord God said, “The man has now become like one of us, knowing good and evil. He must not be allowed to reach out his hand and take also from the tree of life and eat, and live forever.”

              • Hugh says:

                ‘ and live forever.’
                Yes, live physically forever; have an everlasting physical body clothing the sinful spirit which now knows good and evil; and has chosen evil.

                • So there was a tree of life for immortal people, which would cause them to stay immortal.

                  (Why would they need it if they’re immortal?

                  But then it’s taken away after they become mortal?

      • This may also be of interest: “Starlight and time—a further breakthrough.” A stunning new book by a physics professor purports to show more firmly than ever how light from the most distant stars would have reached Earth in a very short time. Reviewed by Carl Wieland.

        • I forgot to add the URL, in the post above, for “Starlight and time—a further breakthrough.” A stunning new book by a physics professor purports to show more firmly than ever how light from the most distant stars would have reached Earth in a very short time. Reviewed by Carl Wieland. The URL is http://creation.com/starlight-and-time-a-further-breakthrough.

        • Perry: Below are the answers to the errors you promote in your reply (above). Also, have you ever thought about debating Dr. Jonathan Sarfati (especially since you attack him above)? Many unbelievers are afraid to do so, including Richard Dawkins, are you afraid to debate him too? I would love to see a debate like this. Let me know, in your reply, if you will debate Dr. Sarfati and I will put him in touch with you to make the arrangements.

          The Fall: a cosmic catastrophe
          Hugh Ross’s blunders on plant death in the Bible
          http://creation.com/the-fall-a-cosmic-catastrophe

          by Jonathan Sarfati, CMI–Australia

          21 February 2005

          Creation/Fall/Redemption

          Dr Hugh Ross is well known for adding billions of years to the Bible, claiming that the creation days were long ages. His view is often called progressive creationism. However, biblical creationists have long pointed out a major problem for this view—that the Bible teaches that death came through sin. Indeed this is foundational to the Gospel (see Understanding death: Answering the question, “Why does God allow bad things to happen?”). But if millions of years are real, then the fossil record must predate sin. But fossils are the remains of dead creatures—therefore, millions of years entails that death predates sin, which in turn entails that death is not the result of sin. This makes God the author of gratuitous death and suffering instead of the righteous Judge who justly enacted punishment for sin (see The god of an old earth: Does the Bible teach that disease, bloodshed, violence and pain have always been ‘part of life’? and Why would a loving God allow death and suffering?).

          This also has baneful consequences for the Gospel. Romans 5:12–19 and 1 Corinthians 15:21–22 clearly teach that human death came because of the Fall. The latter even contrasts the death of the first Adam with the Resurrection from the dead by the Last Adam, Jesus.

          This is a real problem for Ross’s view, because according to dating methods he accepts, there are undoubted human fossils ‘older’ than his date for Adam. And of course, fossilization requires death! See Ethiopian ‘earliest humans’ find: A severe blow to the beliefs of Hugh Ross and similar ‘progressive creationist’ compromise views, about Homo sapiens ‘dated’ at 160,000 years ago with evidence of intelligent cultural activity.

          Ross’ credibility took a further dent with the recent redating of two partial skulls of Homo sapiens that were unearthed in 1967 near the Omo River in southwestern Ethiopia. Radiometric dating, which Ross defends, has now placed them at 195,000 years ago:

          40Ar/39Ar ages on feldspar crystals from pumice clasts within a tuff in Member I below the hominid levels place an older limit of 198 ± 14 kyr (weighted mean age 196 ± 2 kyr) on the hominids. … Our preferred estimate of the age of the Kibish hominids is 195 ± 5 kyr, making them the earliest well-dated anatomically modern humans yet described.1

          Omo I has always been viewed as thoroughly modern in appearance. And although Omo II, which consists of just a skull with no face, has more primitive features, Fleagle maintains that it is still best assigned to H. sapiens, particularly as both skeletons are now thought to be the same age.2
          So undoubtedly modern humans are dated—by methods that Ross advocates—to be far older than his date for Adam. He would do well to abandon his faith in long-age ‘dating’ and repent of his unbelief in the biblical timescale. See Redating Leakey’s Ethiopian human finds: more problems for compromise.

          We have also pointed out the baneful consequences of Ross’s view for the Australian Aborigines. According to radiometric dating, they are older than Ross’s date for the Flood, and even Ross’s dates for Adam allow the possibility that he was younger than the Aborigines. This has the horrifying implication that the Aborigines are not human!

          Cosmic scope of the Fall

          Ross’s problems don’t end there. God gave Adam dominion over creation, so when he fell, the whole creation suffered—see The (second) greatest catastrophe of all time. This is taught in Romans 8:18–25, where the ‘whole creation’ is said to be groaning in pain, because it was ‘subjected to futility’. The late New Testament scholar Dr F.F. Bruce, then Rylands Professor of Biblical Criticism and Exegesis at the University of Manchester, affirms that this passage is indeed speaking of the Curse which fell on the whole creation—the entire universe—as a result of the Fall.3 Bruce also considered who ‘subjected the creation to futility’ and concluded that the text indicated that it was ‘most probably God’, and most unlikely that other commentators could be right when they suggested Satan or Adam.4

          Another expert on commentator on Romans, New Testament scholar C.E.B. Cranfield, likewise made it very clear that ‘creation’ in Romans 8:19–20 was universal: ‘the sum-total of sub-human nature both animate and inanimate.’5 Further, Cranfield explicitly states ‘[t]here is little doubt that Paul has in mind the judgement related in Genesis 3:17–19, which includes (v. 17) the words “cursed is the ground for thy sake.”’,5 thus relating the Fall to the creation outside mankind as well.6

          Yet another commentator on Romans 1–8, James Dunn, wrote:

          The point Paul is presumably making, through somewhat obscure language, is that God followed the logic of his purposed subjecting of creation to man by subjecting it yet further in consequence of man’s fall, so that it might serve as an appropriate context for fallen man; a futile world to engage the futile mind of man. By describing creation’s subjection as ‘unwilling’ Paul maintains the personification of the previous verse. There is an out-of-sortedness, a disjointedness about the created order which makes it a suitable habitation for man at odds with his creator.7
          Ross supporter Norman Geisler also affirmed that the Fall was a cosmic disaster. And more recently, Chuck Colson and Nancy Pearcey gave a good account of the biblical teaching of the origin of death and suffering in their book How Now Shall We Live?

          God is good, and the original creation was good [Genesis 1:31 actually says ‘very good’]. God is not the author of evil. This is a crucial element of Christian teaching … there would also be no basis for fighting against injustice and oppression, against cruelty and corruption, for these, too, would be reflections of God’s own nature, and, therefore, inherent in the world as he created it.

          … Redemption means the restoration and fulfillment of God’s original purposes. [p.194]

          The consequences of sin affect the very order of the universe itself. … the Fall affects all of nature … their rebellion injected disorder into all of creation. [p. 197]

          Every part of God’s handiwork was marred by the human mutiny … At the Fall, every part of creation was plunged into the chaos of sin, and every part cries out for redemption. Only the Christian worldview keeps these two truths in balance: the radical destruction caused by sin and the hope of restoration to the original created goodness. [p.198]8
          Mr Colson is a long-ager, so evidently doesn’t see the implication of what he is writing (Mrs Pearcey certainly used to be a YEC, since she wrote for the Bible Science Newsletter, but seems low-key on the issue now). That is, the fossil record shows the very effects of chaos, cruelty and corruption they say came from the Fall, and wasn’t part of the good creation. Therefore, the fossil record must have come after the Fall, which rules out millions of years. Instead, the globe-covering Flood of Noah’s time would explain many of the massive fossil deposits. See Genesis and catastrophe: The Flood as the major biblical cataclysm.

          Animal death and the Fall

          Part of this creation is the animal kingdom, so this must also have suffered, and the fossil record is stark testimony to that. Yet the Bible clearly teaches that animals were not always being destroyed by cataclysms, and were not always tearing each other to pieces.

          This is shown by the diets that God originally instituted. Gen. 1:29–30 clearly teaches that animals and people were both created vegetarian. As pointed out in the Exposé of Ross’s book: The Genesis Question, Dr Ross accepts that these verses teach human vegetarianism before the Fall, but he is inconsistent in denying the original animal vegetarianism taught in exactly the same words in exactly the same context. We explained this further in this reply to an old-earther.

          Further, even one of Dr Ross’s supporters, apologist Dr Norman Geisler, recognizes this (see how he answered the gripe about animal suffering by the apostate Charles Templeton). We have documented that Basil the Great, John Calvin and John Wesley also understood Genesis 1:29–30 as teaching that animals were all created vegetarian. So it’s Ross’s view that is the aberration.

          Another strong case against carnivory being part of the original creation, also pointed out by Geisler, comes from Isaiah. Isaiah 11:6–9 and 65:25 prophecy that there will be a time in the future with no bloodshed in the animal kingdom. These are famous passages about a lion and calf, wolf and lamb, and a vegetarian lion and a nonharmful viper. Significantly, both passages close with indications that this reflects a more ideal world and the current world does not: ‘They shall not hurt or destroy …’ and ‘They shall do no evil or harm …’.4 These indicate that hurting, harming and destroying animal life would not have been part of a ‘very good’ creation. Commentators such as Dr Alec Motyer, Principal of Trinity College, Bristol, have noted that these passages are a partial restoration to what it was like in Eden:

          There is an ‘Edenic’ element in Isaiah’s thinking (see on 2:4b) … the life of nature itself is transformed. Verses 6–8 offer three facets of the renewed creation and verse 9 is a concluding summary. First, in verse 6 there is the reconciliation of old hostilities, the allaying of old fears; predators (wolf, leopard, lion) and prey (lamb, goat, calf, yearling) are reconciled. So secure is this peace that a youngster can exercise the dominion originally given to humankind. Secondly, in verse 7 there is a change of nature within the beasts themselves: cow and bear eat the same food, as do lion and ox. There is also a change in the very order of things itself: the herbivoral nature of all the creatures points to Eden restored (Gn. 1:29–30). Thirdly, in verse 8 the curse is removed. The enmity between the woman’s seed and the serpent is gone (Gn. 3:15ab). Infant and ‘weaned child’ have nothing to fear from cobra and viper. Finally, in verse 9 the coming Eden is Mount Zion—a Zion which fills the whole earth. Peace (9a), holiness (9b), and ‘knowing the Lord’ (9c) pervades all.9
          The problem for all long-age views is that the fossil record demonstrates carnivory, and Ross dates this to millions of years before the Fall. But this contradicts the clear biblical teaching that animals were not eating each other before the Fall. Geisler has also completely missed this point, so at least Ross is being more consistent when he simply denies that animals were created vegetarian, the way the Bible and Geisler say they were.

          What do creationists mean by ‘no death before the Fall’?

          Many anti-creationists knock down a straw man by simplistically attacking a ‘no death before sin’ statement out of context. That is, they argue that plants and individual cells died before the Fall, e.g. when animals ate plants.However, creationists have often pointed out that ‘no death before sin’ applies to what the Bible calls death, which is not always the way modern biologists use it. The Bible doesn’t talk about plants dying, even though modern biologists do. Rather, the Bible talks about plants withering, for example.

          What is the difference? Answer: the creatures affected by death were those the Bible calls נֶפֶשׁ חַיָּה (nephesh chayyāh). When it refers to man, it is often translated ‘living soul’, but, of other creatures, including fish, it is often translated ‘living creature’. However, it is never applied to plants or invertebrates. Therefore, there is a qualitative difference between the deaths of the (vertebrate) animals called nephesh chayyāh and plant death. This is further supported by the account of the Flood and Ark. The living creatures (nephesh chayyāh) rescued on the Ark did not include plants (or invertebrates)—see How did the animals fit on Noah’s Ark?

          In any case, it should be obvious that plants don’t experience suffering or pain as animals do. But Dr Ross absurdly claimed (Creation and Time, p. 63)

          But even plants suffer when they are eaten. They experience bleeding, bruising, scarring and death. Why is the suffering of plants acceptable and not that of animals?
          It’s hard to believe that Ross wasn’t joking, but he really meant it in all seriousness. But plants don’t have a brain to interpret tissue damage as pain!

          Do plants ‘die’ in the biblical sense?

          Ross’s book The Genesis Question further tries to justify applying ‘death’ to plants in the biblical sense. Somehow he thinks that if he can prove that plants die in the same sense as animals, then he will have undermined the creationist case against animal death before the Fall.

          and by the way, botanists did not originate the claim that plants experience life and death. The Bible said so first, (p. 100)
          He tried to back this up with note 24, p. 125, with the passages Exodus 10:12–17, Job 14:8–10, Psalm 37:2, Matthew 6:28, 30 and John 15:6. So let’s analyze these in turn:

          Ex 10:17 (Pharoah after locusts destroyed crops) ‘Now therefore, forgive my sin, please, only this once, and plead with the LORD your God only to remove this death from me.’

          Note first that this is an uninspired request from the pagan Pharaoh after locusts destroyed the crops. Note that the Bible does not endorse everyone it quotes or every action it records. Biblical inerrancy requires only that people are reported accurately, not that the people are correct. E.g. Psalm 14:1 accurately reports a fool saying something false: ‘The fool says in his heart, “There is no God.”’ Job 2:9 accurately reports Job’s wife saying, ‘Curse God and die,’ but clearly doesn’t endorse such a thing!

          Even more importantly, the results undermine Ross’s claim anyway. Note that Pharaoh says ‘remove this death from me’, and the result was not restoration of the crops (which is the only thing that would support Ross’s claim), but removal of the locusts.
          Ex. 10:19 ‘And the LORD turned the wind into a very strong west wind, which lifted the locusts and drove them into the Red Sea. Not a single locust was left in all the country of Egypt.’ So the locusts were the ones described as ‘death’, i.e. the agent of death , since human and livestock death is a sure result of the destruction of the crops.
          Job 14:8–10 ‘Though its root grow old in the earth, and its stump die in the soil, yet at the scent of water it will bud and put out branches like a young plant. But a man dies and is laid low; man breathes his last, and where is he?’

          This is an absurd passage to try to justify plant death, because clearly this plant is not even dead in the modern biological sense! After all, it can sprout branches again if only there is water available. This passage actually contrasts this ‘death’ with man’s physical death, which is permanent (until the final Resurrection).
          Psalm 37:2 ‘For they will soon fade like the grass and wither like the green herb.’

          This is the sort of thing we point out—plants are described as fading and withering, not dying.
          Matthew 6:28, 30 (Jesus) ‘And why do you worry about clothes? See how the lilies of the field grow. They do not labor or spin. … If that is how God clothes the grass of the field, which is here today and tomorrow is thrown into the fire, will he not much more clothe you, O you of little faith?’

          There is nothing about living or dying here. The NASB has ‘which is alive today ’, but ‘alive’ is in italics to indicate that it has been added by the translators to make sense (in their opinion) and wasn’t in the original language. It is folly to derive biblical doctrine from the opinions of translators.
          John 15:6 ‘If anyone does not abide in me he is thrown away like a branch and withers; and the branches are gathered, thrown into the fire, and burned.’

          Once again, plants are said to wither, just as CMI says. So none of these cases support Ross’s claim, and rather support what CMI has always said.
          Ross’s dishonest debate tactics

          Dr Ross debated creationist astrophysicist Dr Jason Lisle in December 2004 (see summary in Death, dating and the days of creation and my detailed annotations of the full transcript). The moderator, Dr Bob Grant, had already hosted Dr Ross on his show by himself, and Dr Grant seems to be under the same misapprehension:

          Now, in one curious point to me, Dr Lisle if I may ask the question, the idea that food was being consumed or that there was some kind of end of life process for plant or vegetation prior to the fall. That is a thought or an idea introduced into this conversation that perhaps you could respond to that directly.
          Dr Lisle responded

          Of course. And Ross’s mistake here was taking the scientific definition for death and assuming that that’s the same as the biblical definition for life and death. And they’re not the same, you see. In science life is defined in a particular way, but according to Scripture, plants are not alive. The Hebrew word nephesh chayyāh—it’s referring to living souls, and the Bible doesn’t apply that to plants. Plants you can think of as biological machines. They’re not alive in a biblical sense, animals are and human beings are.
          Ross patronizingly replied

          Well, Jason, I’ve refuted that in a thing that’s up on our Reasons.org website where I list a number of passages in the Old Testament where plants are referred to as experiencing life and death. And the interesting thing is that the identical word used to refer to the life and death of humans are also those words used in that context.
          This is pure bluff and bluster. As shown above, Dr Ross has refuted nothing with his biblical citations. And it’s notable that Dr Ross failed to address Dr Lisle’s point that plants are not nephesh chayyāh, also shown above. Instead, Dr Ross continued to ignore this point throughout the debate, and instead continued his ‘snow job’, e.g.:

          Well right and an answer to Isaac [a caller], I mean you really want to look at the entire Bible before you decide what the Bible calls living or dead. For example you can go to Exodus 3–10 where it’s talking about the plagues that are poured down upon Egypt, and there it makes it quite clear that Scripture is saying that plants do experience life and death in the same way the soulish animals do, in the same way that human beings do.
          Here we see Ross’s elephant hurling, trying to give the impression of weighty evidence by citing eight chapters that allegedly support his case. It is a dishonest tactic, since under the time constraints it is impossible to skim through all this to find out what on earth he was talking about. Also, it did not address what Dr Lisle actually argued about plants not being nephesh chayyāh. Instead, Dr Ross implies that there are many references to plant death in these chapters of Exodus. Certainly, the Hebrew for die/death (mût/mavet) is used a number of times in these chapters:

          Ex 4:19 ‘for all the men are dead which sought your life.’
          Ex 4:24 ‘the LORD met him [Moses], and sought to kill him.’
          Ex 7:18 ‘And the fish that is in the river shall die’
          Ex 7:21 ‘And the fish that was in the river died’
          Ex 8:13 ‘the frogs died’
          Ex 8:13 ‘And the LORD did according to the word of Moses. The frogs died out in the houses, the courtyards, and the fields.’
          Ex 9:4 ‘But the LORD will make a distinction between the livestock of Israel and the livestock of Egypt, so that nothing of all that belongs to the people of Israel shall die.’
          Ex 9:6 ‘All the livestock of the Egyptians died, but not one of the livestock of the people of Israel died.’
          Ex 9:7 ‘And Pharaoh sent, and behold, not one of the livestock of Israel was dead.’
          Ex 9:19 ‘for every man and beast that is in the field and is not brought home will die when the hail falls on them.’
          Ex 10:17 (Pharoah after locusts destroyed crops) ‘Now therefore, forgive my sin, please, only this once, and plead with the LORD your God only to remove this death from me.’
          Ex 10:28 ‘Then Pharaoh said to [Moses], “Get away from me; take care never to see my face again, for on the day you see my face you shall die.”’
          So in all these chapters, all but one of these clearly refer to people, livestock, frogs and fish, all nephesh chayyāh. The only one in all this snow-job citation of eight chapters that might be taken as referring to plant death is Ex 10:17. So far from wide application of ‘death’ to plants in the chapters he cites, Ross’s case is based on a single plea from a pagan. And as shown above, even this one is not even applying the word ‘death’ to plants anyway! So Ross hasn’t got the slightest case, but he presumably hoped that no one in the audience would check his learned-sounding bluff.

          Conclusion

          Despite what many people think, the main issue for creation is not the length of creation days or the age of the earth. Rather, the issue is what our authority is—is it God’s written Word, the Bible, or man’s fallible opinions of the history of earth and life on it? And if we use exegesis, i.e. reading things out of the Bible, then we can only find normal-length creation days. It is only with eisegesis, i.e. reading secular long-age ideas into the Bible, that anyone can invent long-age creation ‘days’.

          And from the Bible, we learn that there was no death of any nephesh chayyāh before sin—both humans and animals ate plants, which do not die in the biblical sense. Therefore any fossils must have come after sin. And the Bible spends three whole chapters explaining a watery cataclysm that would explain this—the globe-covering Flood of Noah’s day.

          Therefore the young-earth position is not the primary focus of CMI. Rather it is a corollary of biblical authority—a deduction from the propositional revelation of normal-length creation days and death caused by sin. Long-age views undermine this sin-death causality, and thus have baneful consequences for biblical authority and indeed the Gospel. This is why Refuting Compromise was written. Indeed, the first chapter is on the importance of the right authority, and chapter 6 has much detail on the origin of death and suffering because of sin. http://creation.com/the-fall-a-cosmic-catastrophe

          • Reg,

            I will be happy to debate Mr. Safarti. Let’s do this in 3-4 months, I have much on my plate and it will take time to prepare. Use the contact form and my staff will schedule an opportunity. We need to do this through a credible media channel. I suggest Answers In Genesis.

            Having sat on your blog comment for a few weeks, I do not have time to answer all of this. In principle I should not be expected to respond to material which is simply copied and pasted from another website and is not even your own words and thoughts.

            If you have very specific issues you want to bring up then post them. But I can’t deal with a wholesale copy/paste information dump.

            A few years ago a reader (who was rather obnoxious and I had to ban him from the blog) insisted that I do a critique of Safarti’s book and I never got around to it. Again I’ll be happy to debate Dr. Safarti.

      • Blake Reas says:

        C. John Collins has written very good work concerning Scripture and science. I recommend his books. 🙂

    • Jenny Nicol says:

      [Once again, a NASA space probe is supporting the 6,000-year biblical age of the solar system.] This is a complete fabricated lie. You don’t need to be a biologist to understand that that solar system cannot possibly be 6,000 years old. Your religious brainwashing will not allow you to comprehend the truth.

  6. Mike Godfrey says:

    Hi Perry -could you outline the difference between your approach and that of Intelligent design -I am not seeing a great deal of difference currently -thanks

    • ID ranges from vague about evolution to hostile to evolution. Many times the Discovery institute seems to see little difference between evolution and atheism and almost confuses the two. The ID movement is broadly anti-evolution. (Though it’s a big tent, which you’ll find if you go to any ID type events. You will find a very wide spectrum of views there.)

      I am definitely pro evolution. But I understand evolution as a process engineered by cells, which follows the rules of a language – which, because it is under control of the cell, can be studied, analyzed, reproduced and explained. In other words totally subject to scientific method.

      Neo Darwinism does not meet the standards of the scientific method because is reliance on randomness makes it not replicatable, not systematic. The symptom is all the hand-waving explanations that are really… non-explanations. Darwinism also violates information entropy – which is a severe problem. Not trivial.

      Of course ID at some point always invokes a designer by inference and is content with that. I am not at all opposed to a designer, in fact ultimately I believe in one. But if you can discover a systematic process instead of relying on a designer, science moves forward. Otherwise it does not. So if evolution is true then the universe is an open book and we can learn to our heart’s content. There is a LOT to learn that is being ignored by both sides.

      The fact that we don’t know of any codes that are demonstrably not designed infers a designer. But maybe that’s solvable – so I’m offering a prize for its discovery.

      This blog post does a decent job of expressing why I embrace neither traditional Darwinism nor ID: //cosmicfingerprints.com/larry-moran/

  7. Ryan Nagy says:

    Very interesting ideas and very well-presented. I am a little puzzled as to why atheism was brought into the discussion and why the guest was described as “our atheist guest.” Would that make you, Perry, “our christian guest”? If so, why were you not called that? Is atheism called out because it is assumed to be bad? Relevant to his ideas and their veracity in a way that your christianity is not valid to yours? I am calling it out as it seemed very strange to present him that way.

    Regardless, I think you are correct that neo-darwinism will fall. The idea that we evolved simply as a result of random mutations will slowly fall by the wayside as more and more evidence comes in. When that happens though, it seems to me that you will still not have any proof for the existence of god or a designer.

    And IF you can show some evidence for a designer of some sort – someone or something that got the ball rolling, how will it support your holy books? I get the impression that you are implying (I could be wrong) that proof of a designer is proof of the Judeo-Christian god. I am not seeing the connection.

    Anyway, a good read and interesting ideas. Lynn Margulis and Barbara McClintock’s work are extremely important and need to better known. They were first presented to me in a class on dynamic systems and emergence in a psychology Phd program. This was perhaps 10 years. I have no idea how far (or if) they have spread.

    cheers,

    Ryan

    • The format of the Unbelievable? show is almost always a debate between a Christian and somebody else. So it’s not normally necessary to introduce the Christian as a “Christian.”

    • For an update on claims made by the late Lynn Margulis, see: “Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica”

      Conclusion: The implications for evolution and speciation through acquisition of foreign parts and selected genes to produce new lineages, as proposed by Margulis (2), are heightened by this unusual photosynthetic mollusc.

      Photosynthesis links the sun’s anti-entropic force via Schrodinger to the de novo creation of olfactory receptor genes via RNA-mediated events.

      See also: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors http://tinyurl.com/z6q5joj

      Excerpt: Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998).

  8. PZ Myers directs his minions here instead of to the more extensive discussions at http://tinyurl.com/hhyuuac

    I will add this here for the benefit of his readers.

    Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements http://tinyurl.com/gmqnnlz

    This article links everything currently known about the nutrient-dependent links from atoms to ecosystems. The links from microRNAs to metabolic networks and genetic networks include energy-dependent base pair substitutions that link photosynthesis and RNA-mediated cell type differentiation via the physiology of reproduction in all living genera.

    PZ still seems to think that mutations and evolution can somehow be linked to chromosomal rearrangements, which are manifestations of nutrient-dependent pheromone-controlled reproduction that link species from microbes to modern humans.

    Anyone with ideas like his would be forced to exit any meeting of intelligent serious scientists that I have ever attended. There are more than 45000 indexed publications that detail the links from microRNAs to cell type differentiation in heath and disease. All of them support Perry Marshall’s claims.

    That’s the difference between Perry Marshall and people like PZ Myers. Perry Marshall would like others to look at the experimental evidence of biologically-based cause and effect to determine for themselves whether it makes sense in the light of mutation-driven evolution, or what is known to serious scientists about how atoms to ecosystems are linked to chromosomal rearrangements and biodiversity via RNA-mediated amino acid substitutions.

  9. I’ve followed Perry’s discussions of marketing priniciples, Google AdWords, Marketing DNA, and numerous other topics for years, and I find his thinking particularly sound. I listen to professed atheists as they torture their minds attempting to explain the origins of the universe, the earth, of life, and mankind while maintaining a position of intellectual purity.

    My degree is in physics with graduate studies in electrical engineering and mathematics, but I won’t pretend to be as skilled in the field as Perry, because my career choices moved in a different direction, first as a
    technical staff engineer, then as a writer. I wrote the book “Data Communication Basics” for my employer, and a long list of user manuals for the Unix operating system while a senior technical writer and learning-products engineer.

    My first encounter with the Big Bang and evolution was at age 15 in high school when it was explained by the geology professor at a nearby college in a science fair. The probablility of that first molecule of biological compound “accidentally” coming together struck me as so statistically impossible (3 years before I took engineering statistics at 18) that I immediately discarded the entire idea, though I’m not unwilling to hear others explain the possibility of otherwise. I never have found a credible suggestion of what the conditions were 10 seconds before it happened that made the Big Bang even possible. Maybe it’s my simple thinking from growing up on the farm and seeing life, birth, death all around me among sheep, hogs, cows, horses, cats, dogs, and even people on occasion.

    But there is a huge hole in this entire argument — the big elephant in the room, if you will — that is being ignored, at least to a degree and largely out of necessity, on both sides. I am a practicing Christian, though many evangelicals accuse me of worshipping “the wrong Jesus”. But it leaves me wondering why it’s so easy to know God and have an active, interactive relationship with Him, and so many intellectuals are so unwilling to take that course instead of banging their heads against the evolution wall.

    I’m very familiar with the speed of light problem, and indeed, our understanding and the world, of physics falls apart if you change it. But if God is able to give man the power to “move mountains” (2 Peter 3:8), how can that prevent God from doing a lot of things we don’t know yet in this life, but will later in our eternal experience. God is not constrained by the speed of light. How else could He control the universe?

    And how do we know God is constrained by time? Or that there even is a “beginning” before the universe came to be? Is time even pertinent in his realm? When the powers of the universe obey when he speaks, creating DNA, cells, or anything else is trivial. The structure of the world, the atmosphere and how everything works is a testament to his incredible skill as an engineer — a fact only good engineers can fully
    appreciate. Some of his creations leave me speechless, given their incredible beauty.

    Why is it so absurd that God can take unorganized matter and create a world, then set the sun in its current location along with its planets, then bring water and air into being in their proper places, then introduce life forms, in seven periods of time (of unknown duration)? God does not create worlds out of nothing — He organizes whatever he needs the way He wants for His purposes. He is actively involved in what’s going on in this world even today, yet so many professed believers remain oblivious.

    The questions of this debate are thought provoking. It makes perfect sense that DNA has abilities comparable to error-correcting codes in data packets sent over synchronous data-communication networks (ethernet/Internet). And a cell’s ability to alter its DNA to meet its needs is obviously (to me) connected to intelligence placed there by a caring God who loves his children on this earth, along with his other creations so we can appreciate and be amazed at some of his stunningly beautiful creations, with the challenge to learn to live and take upon ourselves many of his attributes (with His help) so that we can, after this life, continue to learn and create and become more like Him as He has promised (I John 3:2).

    But without altering our approach, we’re doomed to keep banging our heads against philosphical brick walls where one cannot find the true answers because we’re too stubbornly independent to be taught by our very own Creator, our Father, our God, as was so clearly taught by Christ and his Apostles some 2000 years ago, is so willing and anxious to understand truths he’s willing to teach us if we will but let Him.

    But He created us free to use our own wills and live by our own choices. He only holds us accountable for how we use that power. Each of has varying talents and abilities, given us by our Creator. We need no believe or acknowledge. If we act in ignorance, he can fix that in eternity. If a person spends their life doing good, they will no lose the corresponding rewards. A loving God will not condemn his children who act in ignorance of certain truths. So we can continue debating, as man has for millenia.

  10. Jim Serafin says:

    Perry,

    PZ in true form resorted to the “magic wand” of God. No one believes it was magic. The information was front loaded. If not you will have to pay out the prize. (eventually)

    Front loaded Information designed into organisms would fight for survival and adapt as the experiments show. And we now know DNA actively fights against mutations. Another form has just been found making random and chance harder to swallow. New class of DNA repair enzyme discovered – http://tinyurl.com/j47cnc8

    The underlying principle that you brought up should be a universal pursuit. I doubt there is a natural mechanism that can write code and improve by ignoring noise and loss. PZ and company could make money though.

    Denis Noble would agree with you that the cell is the engineer. The death of NeoDarwinism, No Selfish Gene – “The genome… is best described as a database used by organisms to generate the functions that you and I and others study as physiology.” http://tinyurl.com/hgdypyc

  11. James says:

    Red herrings don’t go to heaven either

    They say that pride goeth before a fall. And if you’re Jerry Coyne, every fall goeth before an even bigger fall. The poor guy just never learns. Show him that he’s shot himself in one foot, and in response he’ll shout “Lock and load!” and commence blasting away at the other one. It seems the author of Why Evolution is True has got it into his head that a Darwin Award is something it would be good to win. And this week he’s made another try for the prize.

    The rest:

    http://tinyurl.com/hsptxzx

  12. Samiya Illias says:

    This morning, thanks and praise to God, Facebook suggestion led me to this page, and I’m delighted to read about your work! I have been studying the factual accuracy of the Quran since last year, and have been led to a similar path. I’ve come to understand that changing creation at the genetic level is the most extreme form of corruption, which is why the mighty ancients were punished. My blogposts on Mission of the Messengers and Virgin Birth may be of interest:
    Virgin Birth: http://signsandscience.blogspot.com/2015/10/virgin-birth.html
    Mission of the Messengers I – VI:
    Mission of the Messengers
    Part I: World History & Future Implications http://signsandscience.blogspot.com/2015/06/mission-of-messengers.html
    Part II: Satan’s Enmity: Origin & Objective http://signsandscience.blogspot.com/2015/11/mission-of-messengers-ii.html
    Part III: Adam’s Attempt to Improve upon Allah’s Creation http://signsandscience.blogspot.com/2015/11/mission-of-messengers-iii.html
    Part IV: Balance & Guidance http://signsandscience.blogspot.com/2015/11/mission-of-messengers-iv.html
    Part V: Crime & Punishment http://signsandscience.blogspot.com/2015/11/mission-of-messengers-v.html
    Part VI: Immortality & A Kingdom that Never Decays http://signsandscience.blogspot.com/2015/11/mission-of-messengers-vi.html

    • Re: “…changing creation at the genetic level is the most extreme form of corruption…”

      Sadly, most people do not realize that this is what neo-Darwinists have done. Thank God for those who are introducing others to facts that link atoms to ecosystems. The facts attest to Creation Science.

      With or without proselytizing, those who are interested in learning more about science and about creation can find information like this.

      How Strange Twists in DNA Orchestrate Life
      https://www.quantamagazine.org/20160105-supercoiled-dna/

      People like PZ Myers can attempt to refute what is known to all serious scientists about physics, chemistry, and biologically-based cause and effect. But why? Pseudoscience has never prevailed indefinitely against science.

  13. Age of the earth: 101 evidences for a young age of the earth and the universe
    http://creation.com/age-of-the-earth

  14. JEAN CLAUDE PEREZ says:
  15. Christopher Jones says:

    PZ had me going for a while there, and I had to think over Perry’s position in areas where I thought it was pretty clear. But after an hour or so of me feeling uncomfortable and unsure, suddenly he pulls this out:

    ” I would recommend that he read Princeton’s Nick Lane’s recent books on the subject. Currently what a lot of people are pursuing is this metabolism first model of the origin of life where it’s not a matter of code, it’s a matter of chemistry.”

    And I LOL’d for about a minute in the car. All of his patter sort of crumbled away at once. “Yeah, keep going, PZ, keep looking for metabolism to explain an information problem. That’ll get you real far. Keep trying, though. You’ll get there eventually.”

    Thanks Perry for bringing a live example of a “fundamentalist” atheist at work. He had such a repertoire of misdirection moves to use. Do they do this all the time?

    • Yes. They do this all the time.

      ALSO – if you go to the Unbelievable page where the debate is posted and read the comments, you’ll see PZ’s followers (one or two of them credentialed scientists) protesting loudly about how foolish I am.

      Then… when I try to engage with them on very specific issues…

      They vanish.

      This always happens. This has been quietly going on for ten years on my blog posts, in discussion boards etc. The atheists have no answers that satisfy normal scientific criteria for empirical evidence.

    • RAY says:

      Excellent summary of PZ’s position by Christopher Jones. Thank you Christopher.

  16. PZ “he’s a software person, he’s an electrical engineer, and he’s trying to impose his perspective on biology.”
    Perry: “We build models in science. And all scientific descriptions are models. All scientific descriptions are analogies.”
    A survey of the history of science reveals that all of science proceeds on the basis of assuming scientists will find patterns, regularities and order, that is why science is possible and has revealed so much about the nature of reality. Scientists like PZ don’t seem to appreciate the intelligibility of reality, it’s just assumed. Every scientist will impose his view on the evidence and the honest ones will find if it works or not. When we admit our ideological predispositions we are better equipped to move forward with open eyes. PZ demonstrates a commitment to an unswerving faith in the randomness of nature, he is just as much committed to this assumption, as the thing that he accuses Perry of, ie. he applies/imposes the assumption of randomness to all of his science, not because of evidence for it- but despite the evidence. This is a result of a philosophical commitment to naturalism, not a scientific position. It seems to me that the reality is, that the very success of science in finding these patterns, order and regularities puts the evidence in favour of Perry’s view. The question of code in DNA coupled with the reality that in every other instance where code is, and by inferring from that unbroken pattern, the pursuit inevitably discovers an intelligence behind it- is very telling. It doesn’t seem very scientific or just plain honest for PZ Meyers not to question his imposition of randomicity on this evidence. But it is simply the result of a prior commitment to philosophical naturalism. Of course we theists are also predisposed to expect order, patterns, regularities and finally intelligence behind the natural order, but so far nothing has disapointed that expectation. This indeed was the position of those early scientists who help distill what we now know as “the scientific method”.

  17. adam libman says:

    After listening to PZ, I feel embarrassed for him. I don’t think he was very prepared for this this interview. And his knowledge base isn’t wide enough to properly debate you, Perry. I could tell you went back to main “talking points” without answering the question. That being said, I think future debaters will listen to this interview and decide to not debate you Perry because they don’t want to look stupid. An interesting problem. And if you could find a suitable person to debate, it would make for poor listening because it might get too technical. Again, interesting problem. Also, I find it really interesting that people who discredit you point out that you are an EE guy. That somehow because you are an EE guy, you can’t play with them. I find it funny. Anyway, hope all is well with you. Adam

  18. This may also be of interest: The 10 Best Evidences from Science that Confirm a Young Earth http://tinyurl.com/m94deeu

  19. Keith Allingham says:

    Wow. That was a heck of a debate. I thought PZ was doing very well, and caught Perry on a couple of minor points, but was very much disappointed me when he said “…a code that spontaneously emerged…” – a really ironic statement for a man of science and an atheist. As a Christian, and a bit of a fan of Perry’s, I was actually happy to see this; but to be fair, is there any other answer? Well there is, but not for individuals who embrace science and science only. I too am interested in seeing a reconciliation between science and religion, but we probably won’t get there unless there can be an answer to the question “Where does genetic information come from?” that will satisfy both sides. Thanks to Justin, Perry and PZ for making this happen.

    • Genetic information links atoms to ecosystems, which is the best indicator of where it came from.

      Even if you only look at information in the context of energy, you must invent a big bang story at the dawn of creation. But first you must admit that you cannot explain where the energy came from that went BANG! before everything was created from nothing.

    • Ryan Nagy says:

      “…we probably won’t get there unless there can be an answer to the question “Where does genetic information come from?” that will satisfy both sides.”

      Agreed. To me both the scientific and religious answers are not satisfactory. But what I am not understanding, and as I asked Perry above, how does this all relate to your judeo-christian ideas of god. Let’s assume that you can prove that there was some thing or entity that got the ball rolling or started the process (I do not think you ever will). But let’s assume you do. Now what? You automatically assume that this entity was the god written about in the old and new testament. What is your evidence for that?

      Ryan

    • RAY says:

      Exactly my thought, Keith. There is no such thing as a code that just emerges spontaneously. All codes have design built into them otherwise they would not be a code!

      • Sly says:

        Would you consider snowflakes as having code?
        They have patterns and can vary from flake to flake.
        What is the design built into them?

  20. Jim Munro says:

    I would like to see a future debate tackle this question:

    Is ‘science’ justified in precluding the possibility of a supernatural cause?

    it seems to me that people are unwilling to acknowledge even a remote possibility that ‘GOD did it’ for fear of being seen as ‘unscientific’!
    If GOD did create the heavens and the earth, then ‘science’ has effectively hamstrung itself by refusing to allow ‘supernatural cause’ as a possibility!
    As I see it, accepting this possibility should not in any way hinder continued research into how things work, etc.

    • Godel’s incompleteness theorem: No system can prove its own assumptions.

      http://www.perrymarshall.com/godel

      • Gary Allan says:

        No mathematical system ever proves its own assumptions or they wouldn’t be assumptions. Godel’s incompleteness theorem tells us that in any reasonably complex algebra it will be possible to form statements the truth of which is undecidable.

    • Jonathan Pinchbeck says:

      What happens if the Universe is only matter, energy, the vacuum of space and thought. Thought being behind all structure, relationship, algorithm, encryption in every mathematical abstraction we can observe and recognize in nature (physics, chemistry, biology…etc). The likelihood then is that Intelligence, not the ‘supernatural’, is the prime mover of the Universe and is the only outside influence affecting…perhaps dictating initial operating conditions and then letting nature run its course so to speak. Only a hypothesis…

      • skip says:

        If the universe is as you say, if I understand you correctly, then your words, thoughts arguments and ideas are subject to rearranging themselves in the future where it may result in your position as being gibberish because what you currently call intelligence will later be discovered as being nothing more than random babbling that should have been rooted in the belief that it was guaranteed to change. thus the proper assertion might be that the universe is only currently a random guess with no base or concrete footing to assert anything with any kind of coherent argument other than we are simply experiencing a delusion of random intelligence and will eventually move into another random deluded assumption that we are actually “intelligent” currently. ok, time to cachinnate. I’m a cunctator and I rarely post such random moments of jesting out loud.

        • Jonathan Pinchbeck says:

          Intelligence includes that which we see in cell life, and varies in scale and complexity as we look at varying species. Intelligence has to do with awareness and decision making capability that favors some variation on the task of interaction, self-preservation or propagation. We see this in lower levels in bacterium as well as humans. As humans we analyze and manipulate our physical world to understand from it via experimentation. From this understanding we then impose conditions that favor our survival and further understanding (tools, crafts, medicine, engineering…etc), all of which when communicated to others of our species (language) allows us to profit from it individually and collectively, increasing our power of decision in the Universe and ability to impact it. Natural laws follow rule sets governed by logic, our ability to study and grasp that logic is our connection to some form of Universal Intelligence written in code, essentially mathematics and tautologies. There is intelligence in all facets of the physical world and our intelligence allows us to recognize it, albeit by the bias or lens of our species: our hunger to understand our environment pushed by our survival imperative and ability to do so. To think any of this as some kind of random accident is naïve at best.

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