Evolution: The Untold Story, Part 1

There are two kinds of evolution:

1) There’s the version that you read about in the bookstore. It’s two-thirds science fiction.

2) Then there’s the version that PhD biologists, cancer researchers and genetic engineers use to do their jobs.

The two are entirely different.

Popular books tell you evolution works like this:

“Mutations are the random changes in genes that constitute the raw material for evolution by non-random selection.”

-Richard Dawkins, The Greatest Show on Earth, 2009

Dawkins would have you believe that all you need is the fantastically amazing power of natural selection, and given enough time, through random copying errors, the most extraordinary things become possible.

This is what casual bookstore readers and college freshmen are told. But it’s ridiculously oversimplified and it’s mostly false. It’sdick_and_jane the “Dick and Jane” story of Evolution.

But there’s another version of evolution:

It’s rarely mentioned, or at best glossed over, by the atheist evolution lobby and the mainstream press. Yet it’s incredibly sophisticated and elegant. This is “Real World” evolution.

As you begin to discover Real World Evolution, you find it’s entirely different from the Dick and Jane story you were taught. 98% of people know nothing about this. Today, the first in a series where I share with you the incredible adaptive engineering that’s under the hood of all living things.

Evolution Untold Story #1: How Bacteria Adapt

You probably know that bacteria develop resistance to antibiotics. The more we use antibiotics, the more resistance bacteria develop and the harder it is to kill them. We all know that we must not over-use antibiotics. But has anyone ever told you how bacteria generate this resistance in the first place?

Hint: It doesn’t happen by accident.

You’re fighting off an infection and you’re taking antibiotics. To the bacteria, the antibiotic is poison. It leaks into the bacteria cell wall and begins to kill it. The bacteria says, “This poison is killing me. I have to find a way to pump this out of my system!”

It travels around in your body, hunting for a pump.

It locates a cell somewhere in your body that has a pump. It extracts a copy of that cell’s DNA from a plasmid. It locates the section of the new DNA that codes for a pump, inserts that code into its own existing DNA, and builds a pump.

This is called Horizontal Gene Transfer or HGT. It is one of the most common evolutionary mechanisms. This is “real world evolution.” It’s been observed in labs for 50 years now. Because of HGT, the traditional evolutionary “tree of life” isn’t really a tree, especially among lower organisms. Because of genes being passed back and forth between organisms, it’s more like a web.

If the new pump does its job, then the bacteria can now resist the antibiotic. It now produces other bacteria that inherit the same resistance.

But it also does something else: It finds its bacteria brothers and sisters in your system and gives them the same piece of code!

Now ALL the bacteria in your system have a pump that makes them immune to the antibiotic. Your only chance is to find a more powerful antibiotic or hope your body can find some other way to kill them.

Horizontal Gene Transfer on Video:

Consider what Horizontal Gene Transfer tells you about bacteria:

1. They know what new features they need to survive attack
2. They actively seek out other organisms with those features
3. They exchange and read the DNA of other organisms
4. They analyze the DNA of those organisms
5. They locate the sections of DNA that they need
6. They splice the correct sections of DNA into their own DNA
7. They build entire new complex structures with the instructions in that DNA
8. They evaluate the success of what they’ve done
9. They pass the adaptations along to their offspring
10. They evangelize the newly acquired code to their fellow bacteria

Notice that this does not take thousands of generations. It takes one! Through HGT, an organism can acquire a completely new feature in one step. No gradual accumulation of errors necessary.

Bacteria are not stupid. Invading organisms stage an attack, an arms race against your immune system. Bacteria are as skilled at using code as as any software programmer you’ve ever met.

Hmmm… what tricks could software engineers pick up by studying bacteria?

Your own immune system fights back the exact same way. When you get an immunization shot for tetanus, for example, a weak version of tetanus is injected into your blood stream. Your cells have to “crack the code” of how to kill it. Once they’ve done so, they pass this information to their offspring.

You need to get a new immune shot every 10 years, because after a long periods of time, if your immune cells don’t need the extra code, they’ll discard it. Your cells won’t carry around extra instructions they don’t need.

Single-celled organisms are capable of exchanging DNA with each other, and HGT is massively influential in the development of living things. My friend, Open Source Software is w-a-a-a-a-y older than Linux. It’s been powering nano-machines for 3 billion years!

Organisms share code much the same way musicians and writers and software engineers share riffs and rhythms and programs. The never-ending arms race between prey and predator makes each incredibly robust and ensures the survival of both.

Are you beginning to notice how entirely different this is from the antiquated “random mutation” theory? There’s nothing random about Real World Evolution at all. It’s spectacularly sophisticated. It’s intentional.

The “Dick and Jane” version of evolution is deeply misleading, because it fools you into believing that as long as cells replicate, evolution is somehow inevitable. That it’s bound to happen sooner or later. People try to tell you that natural selection is capable of cleaning up whatever mess is made by haphazard, purposeless accidents.

Not true. Even the most elementary mechanisms of evolution – like Horizontal Gene Transfer – are extraordinary feats of software programming genius. Natural Selection has no creative ability whatsoever. It’s just the final step after the cells have performed their task of innovation.

Organisms evolve much the same way human ideas evolve: By intentional innovation and necessity. By borrowing and recombining existing ideas from the outside to form new ones.

If you’ve witnessed the evolution of English or jazz or computer software or smart phones, then you also understand biological evolution. Because all these things evolve through an identical set of processes: Intentional lending, borrowing, and re-combining of the old to make something new.

By the way, geneticists and other professionals who do cancer research and artificially modify organisms do not splice DNA with a tiny set of tweezers. They employ Horizontal Gene Transfer and other mechanisms I’ll discuss in this series. Scientists set up the experiments, but the cells themselves do the heavy lifting.

And while evolution certainly makes many “fortunate discoveries,” they’re not “accidents” in the usual sense of the word. No more than Thomas Edison’s discovery that carbon is a good filament for a light bulb was an “accident.”

Edison’s light bulb was no accident! He swapped out thousands of materials until he found one that worked. Organisms exchange genes and chromosomes until they find genetic combinations that serve their purposes.

Horizontal Gene Transfer is just one of several amazing, systematic evolutionary mechanisms. It’s not random or accidental, it’s algorithmic. In future installments I’ll share 5 more with you. Stay tuned.

Perry Marshall

Bacterial Conjugation on Video:

National Science Foundation: “One step at a time!” Do organisms change slowly or by leaps and bounds?

Citizendium Encyclopedia: Horizontal Gene Transfer

HGT via Parasites: How Bacteria Can Transfer DNA Between Animals. That’s right – micro-organisms can transfer DNA from one species to another. From Medial News Today.

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115 Comments

levgilman says:

Version #1 is an often misinterpreted shortcut of version #2.
Dawkins recognizes all of the version #2 and explains how it fits version #1.

Consider what Horizontal Gene Transfer tells you about bacteria The list is not what Horizontal Gene Transfer tells about bacteria. It is what YOU tell about bacteria.

8. They evaluate the success of what they’ve done
They do; but they do it by surviving

9. They pass the adaptations along to their offspring
10. They evangelize the newly acquired code to their fellow bacteria

Ones that have survived do it because they have survived.

Up to date, it is enough to explain known results. Still, there is possibility of mutagenesis algorithm evolved for better potential, and gene transfer stimulated by function appreciation rather than by mere survival; even in this case, individual mutations are random in the sense meant by mainstream science.

micro-organisms can transfer DNA from one species to another. From Medial News Today.
It is an old news and doesn’t contradict to Darwinism. By the way, where is the powerful Darwinistic lobby to ban the news?

Version #1 is not a shortcut and it’s not a misinterpretation. It is a bald faced lie and an urban legend. The use of the word “random” anywhere in this context is deceptive and anti-scientific. This word should have been purged from the evolutionary vocabulary 50 years ago.

Version #2 does not fit inside of version #1 because HGT is not random at all. “Random” and “non random” do not mean the same thing. This is an abuse of scientific terminology. Transposition is not random. Symbiogenesis is not random. Genome doubling is not random. Epigenetics is not random. There is nothing random about any of these adaptational changes. They are all systematic and done predictively in response to the environment.

I would be interested to see where Dawkins recognizes version #2 and how he fits this into his claims since “The Selfish Gene” in 1976 that evolutionary mutations are “random.” Horizontal Gene Transfer is never mentioned a single time in Dawkins’ entire tome “The Greatest Show on Earth.” Nor is epigenetics. Nor is symbiogenesis. Nor is transposition. Nor is Ohno’s 2R hypothesis or genome doubling. Correct me if I’m wrong, but so far as I can tell, Dawkins is 100% old school (gradualism and non-directed mutations) and he’s obscuring the issue with a natural selection centric paradigm that is well-known to be obsolete.

The tragedy is that these systematic mechanisms are the most interesting part of evolution!

People are skeptical of evolution for good reasons. It’s not an accident that only 1/3 of Americans believe in evolution. Yes, it’s partly for religious reasons. But it’s also because 100% of human experience tells us that complex machines don’t magically appear, and they don’t improve by random accident. It violates all common sense.

If Dawkins actually explained how evolution works – as I am doing here – then more people would accept a theory of evolution. And they wouldn’t feel as though a philosophy of meaningless chemistry and Darwinian politics was being rammed down their throat.

The reason he doesn’t explain how evolution works is because as soon as he does, people are going to ask a bunch of really inconvenient questions. Like how Horizontal Gene Transfer could accidentally evolve from randomness.

A hypothesis that bacteria only pass on code because they survived is a less effective explanation for fitness than a theory that cells actively promote what works. Such a hypothesis is also supported by the literature. It’s obvious that cells transfer genetic material selectively.

It’s why immunization works. You don’t become immune simply because you survived, or because your immune system survived, but because large numbers of cells in your immune system acquire immunity via HGT. Cells have to be selective about what they promote and accept because otherwise they’d all be bloated with gigabytes of code that they don’t need. The word “selective” is appropriate here and it’s not “natural selection.” It’s intentional filtering.

I would like you to notice that your traditional Darwinian view brings a set of anti-scientific preferences and biases to the table. Listen to yourself: You actively prefer to embrace randomness as an explanation, even though a paradigm of systematic action is by definition more scientific. You are attempting to attach a misleading label of “randomness” to known systematic cellular activities. You seem to exhibit a lack of curiosity as to the details of the exact mechanisms that make HGT possible.

Why?

Are you committed to a purposeless, atheistic paradigm? Or are you willing to follow the evidence where it leads?

mystery says:

I am just a new blogger and I am so much interested about the discussions posted here so I am wondering if randomness is also a miracle that points to God when it goes beyond the mechanisms of order?
1. If God can be reduce to deterministic science and its brute explanation and purpose then what would be the outcome of the idea of God?
2. The way people think of randomness is perhaps pointing to the fact of its deceitfulness. Could this be the result of sin mentioned in the Bible?

Conceptfly says:

This is talking only about adaptation within a species, not evolution. I understand the taught idea that micro-evolution somehow ties to macro, but adaptation should not be taught as evolution unless there was an actual basis to tie it together. In other words, I’m interested to hear how a bacteria turned into a tree and a cat, not how it is programmed from God to learn to adapt to new stimuli.

In future installments I will document mechanisms that produce new species.

wisp says:

:
___________________
|It’s not an accident that
|only 1/3 of Americans
|believe in evolution.
—————————–
I’m not American.
I agree that the geographical distribution of acceptance of Evolution is not accidental. But i don’t know why you’d want to use this fact.
_______________________________
|Yes, it’s partly for religious reasons.
|But it’s also because 100% of human
|experience tells us that complex
|machines don’t magically appear,
|and they don’t improve by random
|accident.
———————————————–
Well, you’re using the term “machine” in a very liberal way.

In any case… Who says that life “magically appears”, but creationists?

Abiogenesis is chemistry. Evolution is pretty much mathematical. I see no magic in any of them.
_____________
|It violates all
|common sense.
——————–
Common sense is what tells me that the world is flat, and the Moon is bigger in the horizon.

If Science was driven by common sense, it would have stopped a long time ago, unable to defeat our own mental bugs.
_______________________________
|If Dawkins actually explained
|how evolution works – as I am
|doing here – then more people
|would accept a theory of evolution.
|And they wouldn’t feel as though
|a philosophy of meaningless
|chemistry and Darwinian politics
|was being rammed down their throat.
———————————————–
You make it sound dramatically violent. But you could say the same thing about lots of scientific facts. Like the fact that matter is mostly empty space.
____________________________________
|The reason he doesn’t explain how
|evolution works is because as soon
|as he does, people are going to ask
|a bunch of really inconvenient questions.
|Like how Horizontal Gene Transfer
|could accidentally evolve from randomness.
——————————————————
What do you mean by “accidentally”?

If you mean “in violation of a carefully laid out plan”, then nobody says it was accidental.

And the process wouldn’t be random, but stochastic.

It is quite wrong trying to explain it from the individual perspective. You need to focus on the point of view of the gene.

We see bacteria selflessly donating genes to other bacteria. And if you ask “How did this selfless mechanism evolve?”, you have focused on the wrong stance of Evolution. It’s not good for the donor. It doesn’t even have to be good for the receiver. This is just one of the ways genes reproduce. Bacteria are their hosts, and they “want” to be in more hosts.

Just change the focus, and you’ll be able to see it (if you want, of course).

Cheers! ^_^

Machine: Self-replicating machine a la Von Neumann.

Dawkins: “Life was a happy chemical accident.” Heard him say it on a Boston Radio station, live in 2005.

The laws of the genetic code are not derivable from the laws of physics and chemistry. See “Information Theory, Evolution and the Origin of Life” by Hubert Yockey (Cambridge University Press, 2005) http://www.amazon.com/gp/product/0521802938?ie=UTF8&tag=httpwwwperryc-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0521802938

“Accident” = chance organization of molecules devoid of any intentional process or agency.

A flat earth is not common sense. People in general have not believed in a flat earth for 2500 years.

Wisp, please refer me to just one successful abiogenesis experiment.

Very interesting, address nothing to origin.

wisp says:

__________________
|Machine: Self-replicating
|machine a la Von Neumann.
—————————————
Oh, so by “machine” you don’t mean “something purposefully assembled by a human being”.

Alright, that’s fine. Then i did see machines arising naturally. They self-replicate, as your quote says.
__________________
|Dawkins: “Life was a happy
|chemical accident.”
—————————————
I’m pretty sure he didn’t mean “in violation of a carefully laid out plan”.

Wouldn’t you agree?
___________________
|The laws of the genetic code
|are not derivable from the laws
|of physics and chemistry.
—————————————-
I’m not sure what that means.

Life IS chemistry. But if you’re going to study it, then yeah, you’ll need more than chemistry. Because the broader scope is more informative and agile when describing its behavior.

In any case, if there’s anything in this universe that’s not bound by Physics, Science has yet to detect it, whether you call it “supernatural” or whatever other name.
________________
|“Accident” = chance
|organization of molecules
|devoid of any intentional
|process or agency.
————————————-
That would cover pretty much everything we know, except for man-made things.
_________________
|A flat earth is not common
|sense. People in general
|have not believed in a flat
|earth for 2500 years.
————————————-
That’s the power of knowledge. People learn, and kiss their common sense preconceived notions good bye.

I love humans. ^_^

I mentioned a flat earth because you would agree. With others i would mention Evolution.
In fact, i sometimes do. They say “Creation is not common sense. You’d have to be a moron.”

I think they miss my point, just like you do.

People grow, and want to distance themselves from old primitive notions. I think we can grow without denying our past.

People who believed the Earth was flat were not necessarily morons. It was common sense. It’s what our senses indicate. You can only overwrite it with knowledge.

Einstein showed us the counter-intuitive fact that simultaneity of events at far distances is another mental bug of ours.

It is an evolved one. It makes perfect sense, if we see it from an evolutionarily point of view. Our mental structure for dealing with temporal events (including seeing time as something different than a dimension) responds to selective pressures.
_______________
|Wisp, please refer me
|to just one successful
|abiogenesis experiment.
———————————–
OK, but who would be the judge of its success?

It would be you, right? =/

Please demonstrate the origin of a naturally occurring self replicating machine. Or the origin of any life from non-life. That is my definition of a successful abiogenesis experiment.

Please show how the laws of the genetic code can be derived from the laws of physics and chemistry.

wisp says:

________________________
|Please demonstrate the origin
|of a naturally occurring self
|replicating machine.
—————————————
Alright.

http://en.wikipedia.org/wiki/Autocatalysis

The sigmoid variation of product concentration in autocatalytic reactions reminds me of the adaptive genetic change. It’s the same that happens to the frequencies of genes in most adaptive variations (in diploid species). The variation starts very slow, it speeds up, and then it’s a slow road to fixation.

It gets slow because of dominance (you probably know what i’m talking about). Selection can’t touch dominant heterozygous, so it can only eliminate recessive homozygous.

Perhaps you won’t want to call autocatalysts “machines”. You’ll probably prefer to reserve that tag for something more supporting of your position. But i don’t see a real difference. None that matters, anyway.
_______________________
|Or the origin of any life from
|non-life. That is my definition
|of a successful abiogenesis
|experiment.
————————————-
Oh… Like when YECs ask for a monkey giving birth to a human… I see.

Do you think our definition of “life” is very relevant? Viruses don’t qualify. Right? So even if i showed you something as extreme as a virus popping out of a chemical soup, you still wouldn’t call it “a success”.

I admit i can’t show you that. I also can’t show you a huge tree sprouting from a small seed. But i can show you steps in both cases.

In any case, demanding to see a process that took a long time in an Earth-sized environment in a little time in a petri dish doesn’t really count as having found a problem with a model.

Am i allowed to be as demanding for the scientific evidence for your position?
Can i ask for you to show me deities tinkering with stuff?
_______________________________
|Please show how the laws of
|the genetic code can be derived
|from the laws of physics and chemistry.
————————————————–
I’m not sure of what you mean.

Are you suggesting that something violates the laws of Physics and Chemistry? That we witness discrete miracles all the time?

A self replicating machine has instructions for building a copy of itself, in digital code. Per Von Neumann. This has none of that. This is just a chemical reaction.

If you don’t see a real difference then you need to educate yourself about the genetic code, my friend. A good start would be watching the “origin of life video” linked at the top of this page.

A virus wouldn’t qualify as life but it would qualify as a naturally occurring code. Do you have any evidence to present?

Look up the genetic code in Wikipedia. It has a table that maps triplets to amino acids, based on a 4-letter alphabet. Show me a law in physics or chemistry that dictates that this would be a 4 letter code based on triplets. Instead of an 8 letter code based on quadruplets or a 2 letter code based on 7 digits (which is what ASCII is).

In all human experience, such codes are only freely chosen by conscious agents.

If you think I am suggesting that something violates the laws of physics and chemistry then you are completely ignorant of my thesis. Watch the video.

I do not mean to sound insulting but you do not seem to even be aware of what the issues are here. I suggest you inform yourself before going forward in this debate.

MSABBAH says:

WISP, A common sense remains valid until a proof comes demonstrating how such a common sense contradicts with another more solidly accepted common sense (or group of common senses), at which event such a common sense will be rejected/discarded. Using common senses to describe facts is accepted because of the shortage in knowledge we human being have. So we human being observe phenomenas, and we make assumptions/theories about them, and some of theses assumptions/theories later become common sense because there is not a better theory to explain that phenomena. The best accepted common sense is the one that lives peacefully (does not contradict) with other common senses.
So the whole life is a system that is built out-of/around common senses which in turn cooperate to make that system what it is. If any common sense comes to break that well-designed system a life is, then you have to re-think about accepting that common sense because it must be wrong.

Old Git Tom says:

Mr Marshall,

a major plank of original Darwinism has always been criticized as a tautology, an empty truism. The theory deals in two base elements, the living animal & its environment. The environment as matter is (relatively) unchanging ‘stuff’, lacking motility, responses or behavior.

The animal or life-form is changeable (evolution) & mobile. Matter is primary here, since it is prior to, & produces, living things, then ‘shapes’ them. This is a logical dualism quite independent of empirical evidence. That is important to Darwin’s theory, since without this logical distinction of life from matter, the theory in incoherent, it makes no sense.

But note the glaring contradiction: life-forms are distinct from dumb, inanimate matter, yet composed of the same stuff as the material environment. Darwin’s original dualism slumps into Dawkins’ monist materialism.

If the defense is that matter can take many different forms, the Darwinian is hoist on his own truism. The non-materialist can smartly respond in that case, that Darwin’s theory loses all sense. If matter can take the shape, form, & behavior of life, then there is not even a starting definition of what a life-form is.

Note again, no amount of research or observation data alleviates this flaw, since a tautology is always true but empty, like one-plus-one-is- two, & not three. To put it another way, the 2-place theory pretends to explain one variable by reference to an invariable. On examination, it consists of two variables – like, you can measure a piece of elastic with an elastic tape, & never get a ‘false’ reading! OGT

objective says:

“1. They know what new features they need to survive attack
2. They actively seek out other organisms with those features

This [and of course many, if not most, other statements of this sort] are unscientific.

How did the ‘working’ code get into the organism that possess it in the first place?

What mechanism of knowledge functions in the organism that goes out to ‘seek it”?

If it knows what it needs the knowledge of all possible threatening scenarions are somehow resident in the genome of the organism under threat??

The organism seeking a cure must surely know where and how to look or does it scan all the trillions of cells in the host’s body??

This behavior is well documented. It is thoroughly scientific. Read http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf

How did the code get into the organism in the first place? That is THE question of biology. I can only tell you that every single fact that we know about computer science indicates that codes are only created by conscious minds.

We know that even the very simplest known bacteria are able to do HGT. Heck, even viruses and their actions are by definition a form of HGT.

What mechanism of knowledge functions in the organism that goes out to ’seek it”? That is one of *the* most important and productive questions in all of biology. But you can’t explore the question if you deny that it’s valid in the first place.

patrikbeno says:

Perry, I may only hope to have more time to respond to all your thesis.

For now, I only want to highlight following:

1) *Random* almost never means pure chance. It means non-deliberate, coincidental, accidental, non-conscious. Also, *random* means something that looks like randomly distributed.

2) The emphasis is never on that *random* part. It is simply not interesting. The emphasis is always on *natural selection*, *genetic variation*, *sexual recombination* and so on.

3) As all non-deliberate unconscious mutations, horizontal/lateral gene transfer, transposition, genome doubling etc cause devastatingly more *harm* than good. The important part here is again the fact that they cause *increase in genetic variation* upon which *natural selection* may operate (and unconsciously select what works and discards the does not).

I am as fascinated as you are by the immune system or the agility of the bacteria.
However, to me, invoking a conscious intelligent purposeful agent does not *explain* anything.

Where you say “Cool, this is beautifully and intelligently designed”,
I say “Cool, this must have naturally evolved somehow, like an eye or something; wonder how?”

Here’s a different interpretation of your observations:

Of course bacteria are stupid. They are not aware of the attack. They lack infrastructure for this.

Therefore, they are unaware of any features they might use. Hence, they do not seek any features. They just do their business as usual: read and exchange any DNA of other organism.

Most of them just do what they always do and get killed by antibiotics.
Some of them just happen to hit & copy the piece of DNA that is helpful in this war-on-antibiotics. They do not know about it. Natural selection let them know about it by simple fact that they survived and reproduced.

99.9% of bacteria must be killed for the success of the remaining 0.1%.

They do not evaluate any success. They lack infrastructure for this.
Natural selection evaluates the success. And the definition of success is a simple one: more surviving bacteria means success, less=failure.

(These are just random brain drops. As I said, I am hoping soon to put together a more coherent response.)

Strength & Honor :-)

In mathematics, according to the dictionary, random means:

1.
proceeding, made, or occurring without definite aim, reason, or pattern: the random selection of numbers.
2.
Statistics . of or characterizing a process of selection in which each item of a set has an equal probability of being chosen.

The mechanisms of evolution are deliberate, non-coincidental, non-accidental, and possibly even conscious.

Your #3 is unsubstantiated.

Bacteria are not stupid. Before you continue to espouse this view, please read “Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology.”
http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf

Question: Which is more effective in constructing a model that explains the efficiency and effectiveness of evolution:

1) Bacteria are stupid and purposeless
2) Bacteria are smart and deliberate

Which is more in keeping with the spirit of science, which is to search for systematic explanations for the way things operate?

You have real plants outside your window. You may have real pets in your house. If you actually watch living things all around you, carefully, and see what they do, rather than merely theorizing about them or forcing a reductionistic paradigm on your observations, what do you actually SEE?

Read the article above. The abstract says:

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell-cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings.

(emphasis mine. This author is far from the only researcher to make this observation.)

Finally, I MUST point out: Your interpretation of Darwinism introduces a bias *against* believing that bacteria “know” how to evolve. All evidence and simple observation indicates that bacteria are very smart. But Darwinism forces you to believe they are stupid.

This is ANTI-SCIENCE.

My friend, I invite you to set aside your Darwinian filters and, for the first time, open your own eyes and SEE how intelligent nature really is. You don’t need scientific papers to tell you this. You can see it in your own garden. Today, I give you permission to use your own eyes and see what is right in front of you.

patrikbeno says:

Perry,

(sorry for a long post)

I am born again atheist, and I like it :-) . I was a sincere believer and a creationist for 15 years. I know it all backwards and I understand how you think. I just don’t agree.

I read your stuff just because your more informed, educated, interesting and provocative. That inspires me, that makes me think about stuff. But deep inside you, between the lines, I recognize the very same pattern: theological thinking.

I do not care about that. I know I cannot convince you, and I do not even try.
I was there once, too.

Now,

***** Luria–Delbrück experiment *****

The Luria–Delbrück experiment demonstrates that in bacteria, genetic mutations arise in the absence of selection, rather than being a response to selection.
…there is no evidence yet for directed mutagenesis: only those mutations that allow the cells to respond to the environmental stress accumulate in a growing population

http://en.wikipedia.org/wiki/Luria%E2%80%93Delbr%C3%BCck_experiment

I.e. bacteria mutate in a constant rate even in a virtually constant ideal environment, producing genetic variation nobody asked for. This mutation rate is unchanged even under a significant selection pressure. Chance that a useful mutation occurs is virtually same whether the selection pressure is or is not present.
If anything can make a difference, it is natural selection, not bacteria itself.

So much for conscious intentional intelligent adaptations of bacteria.

***** Ad. My “unsubstantiated” #3 *****

Antibiotics work by killing whole population of bacteria *before* they get a chance to adapt (mutate). You know that.
If you stop treatment before wiping out entire population of pathogens, you are simply giving bacteria time and resources to mutate. They (remaining population) are no longer under life-threatening stress yet they are living in an environment that is modified enough to provide natural selection from their natural genetic variation.
But you know that, too.

If they were that intelligent, we would not stand a chance with our antibiotics. First bacteria detects an attack, second bacteria finds a defense, rest of population adapts, end of story.

No, you are killing them, and if you do it fast and strong, you will kill them before they adapt. But you know that, too.

How do they adapt?

Their chance to develop useful mutation is determined by time, population size, mutation rate, and a number of blind stupid tests that check the new mutation (usually determined by number of generations).

Furthermore:

Every time a bacteria succeeds, immune system fails.
Every time a immune system succeeds, bacteria fails.
One of them was smarter than the other. Either way, intelligence failed.

The only way intelligence wins is when both sides stop fighting and establish mutual symbiotic relationship between both parties. (This happens, too, but not so often, because of insufficient intelligence .)

So, intelligent? Yes, to a certain level, in a certain sense of the word.
Conscious? On what level? Don’t misuse the word.
Designed? Yes, by natural selection.

/// The mechanisms of evolution are deliberate, non-coincidental, non-accidental, and possibly even conscious.

Now *this* is unsubstantiated.

Deliberate? You mean “Done consciously and intentionally “? Bacteria may be intelligent but they are not conscious (see below). Where there is no consciousness, there cannot be an intent.

Non-coincidental? This implies consciousness and intent. No. Enzyme cannot make a conscious decision. Genes cannot consciously decide anything. All they can do is interact, strictly obeying dynamic unpredictable local rules.

Conscious? Consciousness is an advanced state of self-awareness in a highly developed cognitive analytical intelligence. You need multiple sophisticated sensory systems to provide input from outer world, analytical tool to process input data, to learn from experiences, and flexible memory storage to remember extracted information so that you could use it when your advanced pattern matching engine detects any correlation.

What level of consciousness do you really expect from 5 nm bacteria?

/// 1. The pattern in DNA is a code.
/// 2. All codes we know the origin of are designed.
/// 3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

The only intelligence and consciousness we know is based on matter.
Therefore we have 100% inference that intelligence and consciousness must have somehow evolved from simple low-level building blocks of matter.
And we have 0% inference that it could have existed independent of matter.

Show me an intelligence that is not based on matter. All you need is one.

-patrik

Patrik,

James Shapiro discovered that when bacteria are under stress, their mutation rates increase by a factor of 100,000.

I quote:

“In the first adaptive mutation system described, a Mu prophage can join the 5′ end of araB and the 3′ end of lacZ to generate a hybrid araB- lacZ coding sequence, in effect serving as a model for making multidomain proteins through the actions of transposable elements (Shapiro, 1984; Shapiro & Leach, 1990; Maenhaut-Michel et al., 1997).
These fusions are completely undectectable during normal growth conditions (<10−10), but arise at frequencies as high as 10−5 after prolonged aerobic starvation” (Maenhaut-Michel & Shapiro, 1994).

-from http://shapiro.bsd.uchicago.edu/Shapiro_1999_Genetica.pdf

Experimentation with a number of different mobile element systems has shown that they can be activated temporarily by response to particular conditions. The conditions are quite varied, ranging from blockage of normal chromosome separation during early embryonic develop- ment (McClintock, 1987) to osmotic and other physical stresses associated with protoplast regeneration (Wessler, 1996) to oxidative starvation stress during badaptive mutationQ (Shapiro, 1984; Hall, 1988; Maenhaut-Michel and Shapiro, 1994; McKenzie et al., 2000; Ilves et al., 2001) to mating outside the normal breeding group causing bhybrid dysgenesisQ (Bregliano and Kidwell, 1983; Engels, 1989; O’Neill et al., 1998; Vrana et al., 2000).

From James A. Shapiro, “A 21st Century View of Evolution”: http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf

Barbara McClintock discovered “jumping genes” and that if she damaged chromosomes in corn maize, the cells would repair the damaged chromosome with genetic material from another section of the same plant’s DNA. This is directed mutatgenesis. The literature you are quoting is out of date and incorrect.

Notice that you are imposing on bacteria an a priori assumption that they make blind stupid tests. However from a philosophically neutral point of view, a theory that allows for the possibility that the bacteria are not stupid allows for a more efficient and more effective model of evolution. You’re trying to forbid such a theory. And that’s anti-scientific. Science’s job is to find out how evolution works. Not block researchers from considering answers that make sense.

When I say

“The mechanisms of evolution are deliberate, non-coincidental, non-accidental, and possibly even conscious.”

This is substantiated. Read Shapiro’s papers. Read http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf

You would not be saying what you are saying if you read this paper. I already quoted this earlier in the thread. Please read the relevant material before discussing further.

Let’s address your syllogism:

1. The only intelligence and consciousness we know is based on matter.
2. Therefore we have 100% inference that intelligence and consciousness must have somehow evolved from simple low-level building blocks of matter.
3. And we have 0% inference that it could have existed independent of matter.

The flaw is in #2. We do not have any inference, experiment or experience whatsoever that this actually happens. Which is why you had to say “must have somehow evolved.”

Everything that we know about matter is that if it is not acted upon by outside intelligence, it never produces intelligence. That’s what we know.

If you want to come to any other conclusion then you need to demonstrate code coming from non-living matter. All you need is one.

More importantly, we also know that information is ALWAYS encoded top-down and decoded bottom-up. This is from the OSI 7 layer model in engineering. This alone overturns the “bottom up” theory of evolution as an undirected process. The only way anything language-based can evolve is by following the rules of the code, which are immaterial.

Thus I have shown 100% inference that the genetic code comes from intelligence.

You do not have to agree that the intelligence is from God in order to practice science. But if people deny any possibility of some kind of intelligent input, they end up saying ridiculous things (like others here in this thread) like “DNA isn’t really a code.”

My observation is consistent with the philosophical position of dualism which says that in the relationship between mind and matter, mental phenomena are, in some respects, non-physical. This is reinforced by the fact that information is 100% transferable between media – hard drive / copper cable / fiber optic cable / CD, it’s still the same information.

perrari says:

Dear Mr Marshall,
I have read again and again your challenge to one person or another to give just ONE example of this, that or the other to illustrate a theory regarding natural selection or random mutation.
In this topic you have already asked for “just one successful abiogenesis experiment.”
I have a simple question, “where is the example to show that one species has evolved into another?”
Please do not try to muddy the water by discussing the changes and adaptations that exist WITHIN one species.
There are millions and millions of different species, all simultaneously existing, where is the example of one species giving birth to another. We do not ever see this, we see one species giving birth to the same species. Dogs give birth to dogs, cats to cats, humans to humans, mosquitoes to mosquitoes.
You always allude to evolution as if it were a scientifically proved fact, when in fact last time I checked, it was still only a theory. If you want us all to accept your belief that evolution is true, then at least by your own standards of evidence, you should provide an abundant, possibly even overwhelming amount of factual instances, verified by impartial scientific observation, of one species giving birth to another.
If there is a complete lack of such examples both in the present, and also in the fossil record, then it would be more honest to treat evolution as a possibility, totally unsubstantiated to date, rather than embracing it whole-heartedly because it gives you a platform to try to prove the existence of God to atheists who believe in evolution.
It is a noble endeavour to try to convince others of the Supreme Lord, but if your arguments are based on suppositions that are not verified by the Bible or any other bonafide religious writing, you are on shaky ground.

In future installments of this series I will provide the evidence that you are asking for. Hint: Genome Doubling (polyploidy) is already documented to have generated new species of plants. As is symbiogenesis.

wisp says:

_____________________
|A self replicating machine has
|instructions for building a copy
|of itself, in digital code. Per Von
|Neumann. This has none of that.
————————————————–
Autocatalysts, prions and viruses don’t?

What about cell membranes? The instruction for making them is not in the DNA. A cell membrane serves as a template for more cell membranes. So the “instructions” are there.

It seems to me that you’re labeling reality.

____________
|This is just a
|chemical reaction.
————————–
Sounds like life.

I mean, Biochemistry is a real field.
___________
|If you don’t see
|a real difference
————————
I don’t.
___________
|then you need to
|educate yourself
|vabout the genetic
|code, my friend.
—————————
When people say “genetic code” they talk about correspondence between DNA/mRNA and the proteins (amino acid sequences) they give rise to in living cells.

It’s just an observation of reality, which we choose to label “code”.

If by “code” you mean something with purpose, fine. Then we can drop that word.

Labeling reality doesn’t get you near to demonstrating facts.
______________________
|A good start would be watching
|the “origin of life video” linked
|at the top of this page.
——————————————–
Alright. Watching.

Oh, yeah, i saw that vid.

You say it’s a controversial subject. Perhaps you’re a bit too focused in America?
______________________
|A virus wouldn’t qualify as life
|but it would qualify as a naturally
|occurring code. Do you have any
|evidence to present?
———————————————–
A virus popping out of a chemical soup? Nah.

Can you give me an Earth sized lab and a huge amount of time? ^_^

So, why would a virus qualify, but not a prion? What’s the difference?

___________________
|Look up the genetic code in
|Wikipedia. It has a table that
|maps triplets to amino acids,
|based on a 4-letter alphabet.
—————————————–
4-letters. So it’s not binary. Right?

It CAN be made binary. Just like pretty much anything.
____________________
|Show me a law in physics or
|chemistry that dictates that
|this would be a 4 letter code
|based on triplets. Instead of
|an 8 letter code based on
|quadruplets or a 2 letter code
|based on 7 digits (which is
|what ASCII is).
|In all human experience, such
|codes are only freely chosen
|by conscious agents.
———————————————-
Sounds like you can do the same thing with a golf ball on a particular leaf of grass. You could ask me to show you a physical law that dictates that it should land on that particular leaf of grass, and if i fail to do so you could claim that someone intended for it to land exactly there.

And, by the way, what you say about human experience only applies to humans. You should have said (even if i still disagree with the statement) “In all human experience, such codes are only freely chosen by HUMANS”.

I mean… Do you have any reasons to diminish the accuracy of your experience?
_______________________
|If you think I am suggesting that
|something violates the laws of
|physics and chemistry then you
|are completely ignorant of my
|thesis. Watch the video.
———————————————-
I did. But, unless you’re suggesting that, i don’t see what sense it makes to ask for me to show you a physical law that would determine the way some particular aspect of life is.

It doesn’t sound like a pertinent request.

You can take just about anything and ask for a physical law that dictates the way it is, and claim that someone willed it to be that way when they fail to show you exactly that.

In reality, processes are much more complex than the physical laws we learn, which are simplifications.
Take anything complex enough (which you can find pretty much anywhere), and the laws we use to describe things will fail to make an accurate prediction about its behavior. Which doesn’t mean we should shun them.

Like the clouds you mention in your video. You can watch any cloud and ask for a physical law that dictates for it to be that exact shape. Nobody can give you that. And you don’t claim someone designed it that way just because you can find a physical law that predicts cloud shapes with that level of accuracy.
________________________
|I do not mean to sound insulting
|but you do not seem to even be
|aware of what the issues are here.
|I suggest you inform yourself before
|going forward in this debate.
—————————————————
Still watching your video (again). You pointed out how ridiculous it was to believe that the hand could form by accident. So it looks like you haven’t been informing yourself for a very long time.

You also talk about rearranging fossils to make them tell different stories. Do you think that’s the way they deal with fossils?
I mean… They found the Tiktaalik. The exact morphology in the exact location in the exact layer. That’s a pretty solid confirmation of what we thought. So it looks like we CAN know some stuff. Someone was definitely right about something.

You talk about how a sheet of music represents music. You point out that there is a plan and the plan is implemented.
Well, we KNOW there is a plan, because we KNOW people write music. That’s it.

I bet i can show you stuff that could confuse you. You wouldn’t know if a computer or a person did it. That includes poetry.

The fact that words or music can be written down is not what we use to know there was a plan.
We can take any correspondence between two things and call it “a code”.

Just like there’s a correspondence between tri-nucleotide sequences on one hand, and amino acids on the other, doesn’t mean someone willed for it to be that particular way.

In fact, we KNOW it didn’t have to be that particular way (called the “standard code”), because there are other correspondences (other “codes”).

So if you ask me for a physical law that says it should be like it is, i can safely tell you that it didn’t have to be that particular way, because as a matter of fact it ISN’T always that way.

You say a map is a code. Well, a rolling stone on a hill could conceivably leave a clear print of some part of it as it goes down. You can call it “a map”. You can call it “a code”. You can call it “information”.

It DOES contain information on the shape and irregularities of the stone that left the print.

Why is a map of Washington more like a code? Is it the scale? Or is it the fact that you KNOW that people make maps?

wisp says:

In your video you also talk about the language of DNA.

I’ve heard the syntax claim plenty of times. There is no such a thing in the DNA.

Did you know that nylonase came about as the result of a frameshift mutation? How can you reconcile that fact with the syntax claim?

You say DNA is a code because it’s symbolic. If by “symbolic” you’re implying that someone wanted to convey something, then you’ve indulged in the logical fallacy of the petitio principii (or begging the question). Meaning that your preferred conclusion is contained in your premise.

If your definition of “symbol” implies intelligence, then you have no reasons to assume that DNA contains any.

None that i have seen, at least. Nothing but labeling reality and making language analogies.

You don’t get to use the fact that someone called it “a code” in order to demonstrate something. It’s the equivocation fallacy. The oldest in the book.

Feathers are light.
Light can’t be dark.
Therefore, feathers can’t be dark.

By the way, you asked me again if i had evidence to present (implying that you’d only accept life or at least viruses forming spontaneously from simpler chemicals). I had already told you that i couldn’t (although i can show you steps, just like with steps from seed to tree). And i pointed out that it was like when creationists ask for us to show them a monkey giving birth to a human.

And you didn’t answer my question: Am i allowed to be as demanding for the scientific evidence for your position?
Can i ask for you to show me deities tinkering with stuff?

Wisp,

You need to apprise yourself of the literature that explains why DNA is a code. This is no fallacy. This is precisely what Watson and Crick discovered in 1953.

“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)

See

“The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics.” SUNGCHUL Jl. Department of Pharmacology and Toxicology, Rutgers University
http://www.scribd.com/doc/3040594/The-Linguistics-of-DNA-Words-Sentences-Grammar-Phonetics-and-Semantics

You can be as demanding as you want with anything I put on my website. Ultimately it reduces to this:

1. The pattern in DNA is a code.

2. All codes we know the origin of are designed.

3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

If you want to dislodge my syllogism, then show me a naturally occurring code. All you need is one.

wisp says:

You need to apprise yourself of the literature that explains why DNA is a code. This is no fallacy.

Yeah, look… It’s really easy to say that the other guy doesn’t know enough. I bet you don’t tell that to people when they agree with you.

Do you want to call it “code”? Fine. I don’t care.

Do you want me to show you one? Fine. H2O.
It doesn’t work because it wasn’t made by a mind? Fine. Then DNA doesn’t either, unless you demonstrate it.

I’m not swayed by word games. I’m swayed by facts.

If you say DNA has “Sentences and grammar”, well, tell me how does that work with frameshift mutations.

I already asked you. You didn’t answer.

Do you accept that Nylonase came about as the result of a frameshift mutation?

Wisp,

Nylonase did not arise purely as a result of a single frameshift mutation. It arose as a combination of transposition and horizontal gene transfer. And possibly epigenetics.

Show me how H20 is an encoding / decoding system. Use the format at http://www.cosmicfingerprints.com/blog/solve. Label the parts, the encoding and decoding tables.

A computer equivalent of a frameshift mutation would be when ASCII letters A-B 1000001-1000010 are read as 0000011 (which is the number 3).

Frameshift mutations do not produce significant improvements in computer applications and they’re not sufficient to explain evolution of new features.

Also, the redundancy of the genetic code is specifically optimized to minimize the effect of frameshift mutations. This is well documented. ww.springerlink.com/index/gc2uarjxfl6307vp.pdf

objective says:

“Perry Marshall says:
Comment Link
Wisp,

You need to apprise yourself of the literature that explains why DNA is a code. This is no fallacy. This is precisely what Watson and Crick discovered in 1953.”

You may as well say that Fe is a code or Cl or helium or H2O.

So who designed the code of the coder? An uncoded coder? An immovable mover???

Who designed the intelligent designer??? Some superior designer???

You are funny but what is even funnier is that nobody is able to refute your gibberish.

Pfffft.

The reason you think that what I say is gibberish is because you don’t understand what the genetic code is or what is meant by the technical term “code.”

I have thoroughly an exhaustively explained this 1-5 years ago at http://www.cosmicfingerprints.com/faq and http://www.cosmicfingerprints.com/infidels. No need to repeat it here. It’s explained in literally 1000 biology and genetics books. GGG is not Glycine. It is symbolic instructions to make Glycine encoded as 3 guanine base pairs in a row.

Fe and Cl and Helium and H20 (the letters you are reading on your screen right now) are codes for what we call iron and chlorine and water. However iron itself and chlorine itself are not codes. I repeat: You need to apprise yourself of the literature that explains why DNA is a code. This is no fallacy. This is precisely what Watson and Crick discovered in 1953.

perrari says:

Uh oh, I’m starting to get that familiar queasy feeling in my stomach.

If the evidence that you are going to serve up consists of scientific papers, researchers findings and ‘well-documented’ case studies and discoveries, then I humbly request you to swear on a stack of Bibles (your choice of denomination), that all and every evidence that you present will be the truth, the whole truth and nothing but the truth.

We do not need any more scientific break-throughs preceded by the usual

“Previously it was thought that………………….blah blah,…………but we NOW know that…………….blah blah blah.

If you have proof for your concept of evolution then let it be carved in stone and fixed for all time in all situations. Any future adaptation, modification or change will invalidate it.

Do you have enough faith in the people you will be quoting to stand by their conclusions now and forever more, or is there the possibility that things may change at some point in the future, as our understanding deepens?

The bottom line is…….in whom do you ultimately trust?

The scientific community of the Western world?
Your own ability to sift evidence and conclude?
The revealed word of God through His authorized representative?

Shoshone says:

Did you know that human beings have 12 strands of DNA?
Most of what is considered junk DNA are parts of those twelve strands?
That Russian Scientists found our DNA to be a super conductor that could work at body temperature and when pulsed with sound frequencies and light could influence weather patterns, remote healing , telepathy, activated worm holes in the space time continuum, set up magnetic fields around the individual cells, and
reacted to language most specifically.
Did you know that the evolutionary path of humanity points to only one conclusion
natural evolution based upon humanity’s level of development could not be possible especially with 12 strands of DNA. What they suggest is that we were seeded from somewhere else and that with all of our DNA functioning we are a God race. Not only does God exist but our DNA is proof positive that God is us.
We are all part of the God mind. Furthermore science today is completely handicapped by the intentional separation of science and spiritual understanding and metaphysics that was available in ancient times when access to that knowledge was destroyed, hidden and suppressed by different factions who used religious dogma to get control humanity. It may sound fantastic but it won’t for very long because times are rapidly changing and life as we thought we knew it will never be the same. Did you know that?

joe says:

Quote “You are funny but what is even funnier is that nobody is able to refute your gibberish. ”

wrong…. you can, just solve the The Atheist’s Riddle :)

objective says:

Joe, you mean this one??


1) DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism.
2) All codes are created by a conscious mind; there is no natural process known to science that creates coded information.
3) Therefore DNA was designed by a mind.

If you can provide an empirical example of a code or language that occurs naturally, you’ve toppled my proof. All you need is one.

Perry Marshall

It is actually a number of “riddles” but obviously only by virtue of the undefined concepts and equivocations that are used. If DNA is a code then what is a code and how does it differ from the chemical structure that is supposed to contain it???? what is information and how is it contained in the code??? what is consciousness and what is a mind?
By using the same method as that used for structuring the so-called riddle we may argue that H20 isnt simply a chemical structure:” it is a code, a language and an information storage mechanism.” Therefor DNA and H20 share idnetical attributes and are therefor equivalent : H20=DNA.

To assert that all codes are created by a conscious mind as if a conscious mind functions in the absence of matter (DNA, carbon water etc.) is interesting nonsense believed by Descartes and many other philosophers and religious people but hardly rationally sustainable except perhaps from a null hypothesis.
It further begs the question of what consciousness is …what is meant by the term??? Is it something that is added to matter or is matter added to it?? Marshall seems to support the latter because he states “DNA was created by a mind”. He fails (or is that neglect ) to explain what a mind is and how it functions in the absence of DNA.

His so-called riddle is only a riddle because he depends on his listeners to accept the equivocations and bad logic.

Now let me see if he will post this after he has moderated it.

What is a mind? Look it up in the dictionary.

see http://www.cosmicfingerprints.com/blog/solve for a point-by-point, detailed specification on how to solve the “atheist’s riddle.” If you can solve it I’ll post the results on my website in the designated space and write you a check for $10,000. Pass or fail, any submission you enter will be posted at http://www.cosmicfingerprints.com/submissions/

wisp says:

Let’s see…

1) DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism.
2) All codes are created by a conscious mind; there is no natural process known to science that creates coded information.
3) Therefore DNA was designed by a mind.

1) Unwarranted assertion.
2) Diminished claim (you mean “by humans”).
3) Non sequitur.

Old Git Tom says:

Objective,

philosophically, materialistic science is confounded by another, similar problem.

We can only adequately understand the (material?) universe via human intelligence.
If human intelligence is a part of the universe, how can we trust its objectivity?
If intelligence is separate from its study object, the universe, where does it come from? Where reside? OGT

objective says:

OGT,

You treat the term *intelligence* as Perry treats the terms *consciousness, information, code*.

Intelligence is not an existent but the activity of chemical structures. The same applies to the terms consciousness, information and code.

The functional unit in biology is the cell and the cell consists of and functions by means of molecular structures.

Intelligence is not *seperate* from its object as I noted above. It is the name of the output of cellular functionality.

How to trust our objectivity? The term *trust* is not applicable in the context of the meaning of objectivity. The short answer is that you do not trust it. YOu discover it.

Perry Marshall.

I had a look at your point by point request to refute your proposition. Actually copied it and pasted in MSW with the objective of doing just that.

But having read it I realised that you ask that “the system” must not be designed by humans or exist in a biological system BUT its origin must be natural.

Thus I realised that you are claiming that such a system exists somewhere in nature but you dont know where or how. You do not even know what it looks like or how it functions. Yet you claim it exists.

Thus you are saying: “since the origin of hydrogen and oxygen isn’t known it must have some intelligent source in the form of a code that designed it. Prove that such an intelligence exists that created the code. But your proof cannot be designed by you or any other biological or physical structure – that does not count. It must however conform to some very specific coding parameters known to progammers and be able to be tested by the scientific method”

You may as well ask: prove that a non existent exists without using the material available in the universe.

I am not claiming that such a system exists. I doubt that it exists. I’m outlining a test by which a person could demonstrate that such a system exists.

I am not saying anything about hydrogen and oxygen. I’m talking about the genetic code, or any kind of code. I’m asking for an experiment that produces codes via natural, physical processes without someone “cheating.”

Many people are familiar with the Miller-Urey experiment. MIller and Urey put chemicals in a tank, subjected them to certain conditions and they got certain compounds to emerge.

If that same experiment had produced codes, without the codes being designed or specified in advance, then the Miller-Urey experiment would satisfy my criteria.

joe says:

I dont think the example of H2O proves that its a code. If you have a glass of water there is nothing in there (eg a genetic type code ) that says “this is what you have to do to make the contents of the glass (the water) H2O forms by a chemical bond, not something in the atoms that tells the atoms what to do.

from Wikipedia…
A chemical bond is an attraction between atoms or molecules that allows the formation of chemical compounds

To me the genetic code in DNA is a real code. Just like Morse Code is a code that uses dot and dashes to make words. Morse Code uses rules to make the code work, The genetic code in DNA uses the same principle and rules of a code and not chemical bonding.

from Wikipedia…
The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells

I don’t think the code in DNA proves it was coded by a “god”, BUT to me it dose show it was not put together not by random mutations over time. Also no proof has been demonstrated to show this is the way that it happened anyway. Its just the most accepted theory. (don’t believe me then find the proof that shows its 100% proven to be true because I cant find the papers)
Its a bit like the big bang theory, that’s the most accepted theory of how the universe came into existence, but there is also string theory with its branes and extra dimensions that’s also pointing in the right direction as well.

I see the current theory of evolution has the same problem as Quantum physics and General relativity physics being incompatible, for a general theory of everything in physics. The theory of evolution we have today explains the word we see (the big) with our eyes perfect, like General relativity dose for the big. But it starts to break when it tries to explain the first cells (the small).
The evolutionarily theories they have now seem to point to more problems then it dose in answering them. Our evolution started with the birth of the universe we live in, and the Molecules to Man theory of evolution by random events over time to create what we see around us today, dose my head in, how could that be a theory at all, let alone to be the golden rule of how we got to this point in time.

My take on it all … To only have a “naturalistic view only” of science is wrong I like MICHAEL J. ВЕНЕ
view about it in “Darwins black box”

Imagine a room in which a body lies crushed, flat as a pancake. A dozen

detectives crawl around, examining the floor with magnifying glasses for

any clue to the identity of the perpetrator. In the middle of the room, next

to the body, stands a large, gray elephant. The detectives carefully avoid

bumping into the pachyderm’s legs as they crawl, and never even glance

at it. Over time the detectives get frustrated with their lack of progress

but resolutely press on, looking even more closely at the floor. You see,

textbooks say detectives must «get their man,» so they never consider

elephants. There is an elephant in the roomful of scientists who are

trying to explain the development of life. The elephant is labeled

«intelligent design.»

Most people hate the intelligent design theory NOT because of lack off evidence in the theories (they have some good arguments about the current accepted theory of Darwinian evolution) Most just hate it because it also has RELIGION tagged to it as well.
The Law of Biogenesis states that life arises from pre-existing life, not from nonliving material. Now think about that and ask yourself “is the life we see around us today” here because of the current theory of Darwinian evolution, meaning all we see in the universe is the result of random unrelated/chance events and life spontaneously coming into being from nonliving matter. The most accepted view.
Or do we see a universe and the life in it, has its evolutionary path set on autopilot following the rules and codes that were designed for it. (the complete opposite of Darwinian evolution), The most hated view in science.
How is that question and view unscientific and religious dogma ????

The “how we got here” and “how did the universe get here” and more importantly what is outside of it, is the biggest question of man kind. And to say anyone theory has preference over the other is not true science, its science with ego. True science takes all DATA and then follows that DATA wherever it may lead, not stop at the border of “we have a totally Naturalistic only view of the universe”.

I bet the bigger picture of life and the universe is bigger than we will ever imagine and maybe we will never have the real truth.
Don’t forget we live in a 3D universe with a thing called time, and looking at all that data with only our senses to guide us, and the way we interpret that DATA is also influenced by our own egotistic world view.
Live and look at the world around you with a true open mind try and look at the other side of the coin or view. I did, I looked at the “design view” and I came to believe that it dose point to the beginning of the universe and the life in it as being “designed” that way from the beginning, and not the result of chance and random events and mutations overtime, what is “time” anyway, oh that’s right its the Darwinian God, ;)

Look at the positive side of a “Designed for life Universe” life WILL be everywhere. where it can evolve, it will by using its built in instruction set. This to me is the best answer to “is there life outside of earth” this view of mine points to it being part of the universes law, and if they do find life to me will prove that life was designed to evolve with the universe and not an after effect caused by a one off freak event.

Dose this view mean I believe in a Christian/Hindu/Buddhist ect ect or the Giant Spaghetti Monster type god??? or even if that DATA proves to me there is that type of god, no it just shows I don’t accept the mutation/random/chance events view also. That’s my egotistic world view at the moment with the data and facts as I understand them :) cheers :)

Karlitos39 says:

In your challenge to Athiests, you say that there is no known natural example of the encoding and decoding of information in a top down bottom up manner. Isn’t the that what human imagination, discursive reasoning process, thinking, is?

wisp says:

1) DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism.
2) All codes are created by a conscious mind; there is no natural process known to science that creates coded information.
3) Therefore DNA was designed by a mind.

1) Unwarranted assertion if you’re talking about anything real. Otherwise, it’s just the equivocation fallacy.

2) Diminished claim (you mean “by humans”).

3) Non seqvitvr.

The whole thing seems like three fallacies.
This syllogism contains only one (equivocation):

Feathers are light.
Light can’t be dark.
Therefore, feathers can’t be dark.

Our words are conventional things. We need to talk about real things.

Moreover, EVEN if the two premises were correct, the conclusion is still a non seqvitvr. From the fact that we’ve only known humans doing a certain thing it does not follow that only humans (or “conscious entities”, if we diminish that claim) are able to produce it.

Let’s say that, in all of human experience, only humans are able to polish things. Then we find out that water can do it too.

Can we conclude that water is a conscious entity, and that a pebble demonstrates it?

The version of my syllogism that you are working from is valid, but this one is clearer:

1. The pattern in DNA is a code.

2. All codes we know the origin of are designed.

3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

(1) If you disagree with this then you are in opposition to all scientific consensus on this topic since the 1960′s. Again I recommend that you apprise yourself of the literature and why the Genetic Code is literally a code.

(2) Show me a code that’s not designed. All you need is one.

(3) If all known codes are designed then the logical inference is that the one code we don’t know the origin of is also designed. You are free to reject inference as a means of arriving at conclusions. Just understand that you discard the entire scientific method by doing so. An identical process of inference was used to form existing theories about evolution, gravity, thermodynamics and magnetic fields.

Your syllogism

Feathers are light.
Light can’t be dark.
Therefore, feathers can’t be dark.

Is not a syllogism. It makes no sense.

You are demonstrating a lack of knowledge of the origin of the term “genetic code” and a lack of knowledge of inductive reasoning and syllogisms. When you can demonstrate familiarity with these concepts I will be happy to continue this thread.

Yes, you’re right, water can polish pebbles. If you can demonstrate that codes originate from anything other than intelligent sentient beings then you’ve overturned my syllogism.

wisp says:

1. The pattern in DNA is a code.
2. All codes we know the origin of
are designed.
3. Therefore we have 100% inference
that DNA is designed and 0% inference
that it is not.
(1) If you disagree with this then you
are in opposition to all scientific
consensus on this topic since the
1960’s. Again I recommend that
you apprise yourself of the literature
and why the Genetic Code is literally
a code.

The argument from authority can be somewhat convincing sometimes. But you’re talking about a word. Not about a fact.

I really don’t think it’s too important if you call it a “code” or not. I would prefer to talk about the facts those words are naming.

I repeat my previous answer to this:

When people say “genetic code” they talk about a correspondence between DNA/mRNA and the proteins (amino acid sequences) they give rise to in living cells.
It’s just an observation of reality, which we choose to label “code”.

If by “code” you mean something with purpose, then you need to demonstrate this.
Labeling reality doesn’t get you near to demonstrating facts.

When you say “genetic code” you can also be talking about this:

That’s a code alright. And it was man-made.

When it comes to facts, the scientific consensus is that DNA is not designed.

So i’m against a scientific consensus regarding the use of a word (i’m not, i really just don’t care much for words), and you’re against a scientific consensus regarding facts.

(2) Show me a code that’s not designed.
All you need is one.

Fine: The genetic code.

You can’t just invert the onvs probandi with word play. Show me the facts that make you say it’s designed, instead of just saying “it’s called a ‘code’”.

(3) If all known codes are
designed then the logical
inference is that the one
code we don’t know the
origin of is also designed.

It’s not. But even if it were, if by “code” you try to encompass naturally occurring DNA (or RNA, or proteins) too, then i’m not prepared to assume your if. I would like a demonstration that it’s designed.

You’re just trying to invert the onvs probandi.

If by “code” you mean “something made by a conscious entity”, then we can’t give DNA that name before you demonstrate that it was.

Where are the facts that demonstrate this?

You are free to reject inference
as a means of arriving at conclusions.
Just understand that you discard the
entire scientific method by doing so.

Therefore, water is consciously polishing pebbles.

It doesn’t work like that.

Inference is fine. You’re just using word games.

Your syllogism
Feathers are light.
Light can’t be dark.
Therefore, feathers can’t be dark.
Is not a syllogism. It makes no sense.

It IS a syllogism. It’s not valid because it indulges in the equivocation fallacy (which involves giving a word more than one meaning).

That’s what you do when you say “code”.

You are demonstrating a lack of knowledge
of the origin of the term “genetic code” and
a lack of knowledge of inductive reasoning
and syllogisms. When you can demonstrate
familiarity with these concepts I will be happy
to continue this thread.

Familiarity that would only be demonstrated if i agreed with you, probably.

You give lectures. You have a site dedicated to this issue. I have a difficult time buying the “Because you don’t know enough” clause.

Are your site and lectures addressed to people who know more than me?

When i explain human evolution to people (not that i’m suggesting you deny it), i don’t tell them “Because we’re apes. No, really. Investigate for yourself and come back.” I show them what’s behind the tag “ape”. I show them facts.

Yes, you’re right, water
can polish pebbles. If
you can demonstrate
that codes originate from
anything other than intelligent
sentient beings then you’ve
overturned my syllogism.

What? Are you suggesting that water is not conscious? Why? I used your same syllogism to demonstrate that it is. And you just assumed that it isn’t.

And you keep asking me to make a factual demonstration of something purely conceptual.

I mentioned prions. You discarded them. I don’t know why. What do i have to demonstrate? A symbolic language? I don’t think DNA possesses any. How could nylonase have been produced from a frameshift mutation otherwise?

The definition of DNA as a code is universal in the literature because base pairs are encoded into messenger RNA and decoded into proteins by the Ribosomes (Yockey, 2005). This process corresponds to Claude Shannon’s model of digital communication in his paper “A Mathematical Theory of Communication.”

All you have to do to verify this is type something like

claude shannon information dna
into http://scholar.google.com/

and start reading the 2000+ scientific papers that come up. The word “code” has a strict technical meaning within biology, computer science and electrical engineering. It means the exact same thing in all three disciplines. It is not an accident that all scientific literature refers to the genetic code as a code.

Words express facts and concrete realities. If you wish to dismiss an argument because it’s constructed with words, then you contradict yourself because you are using words to construct your own argument.

The facts that demonstrate that DNA is a code are easily found in the thousands of papers you will find on Google scholar. Pick one and start reading. A good book is “Information Theory, Evolution and the Origin of Life” by Hubert Yockey (Cambridge University Press, 2005) http://www.amazon.com/gp/product/0521802938?ie=UTF8&tag=httpwwwperryc-20&linkCode=as2&camp=1789&creative=390957&creativeASIN=0521802938. Or look up “Genetic Code” in Wikipedia.

You think I am playing word games because you do not know what these words mean or why these words are used. As we talk I get the impression that you are not schooled in biology or in any kind of engineering discipline. Perhaps as an atheist you think it is impossible that well known scientific facts could stand in opposition to your chosen worldview.

I suggest you apprise yourself of the literature. In any case I can assure you that you will get nowhere trying to argue that DNA is not a code.

You cannot use DNA as an example of a naturally occurring code because do not know the origin of the genetic code. You also cannot use it as an example of a code if you think it’s not actually a code in the first place. I suggest you pick a position and stick with it.

Show me a scientific experiment that generates genetic code from non-living matter and you will have proved your point and overturned my argument. You will also win a Nobel prize and worldwide acclaim.

The word “code” in a technical context has only one meaning. This is why Yockey said, “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)

If people who know more than you can show a flaw in my argument, bring them here. I have not refused anyone in 5+ years of this debate. See http://www.cosmicfingerprints.com/infidels

Codes are not purely conceptual. You have 750MB of code in every single cell of your body. You have code in the computer you are reading right now.

If you think that prions are codes, then fill in the table at http://www.cosmicfingerprints.com/blog/solve and show that they constitute a formal digital encoding/decoding system.

Yes, you have to demonstrate a symbolic language. CD’s have symbolic language, as do hard drives and the Rosetta Stone. As does DNA. The computer screen in front of you is a factual demonstration of something conceptual.

Nylonase was produced by a process such as I describe in this very blog post I wrote above (a combination of horizontal gene transfer and transposition), not by a frameshift mutation.

patrikbeno says:

Perry, do I understand correctly that you deny the evolution by frameshift mutation? (Among other things, of course)

I deny that frameshift mutations all by themselves can generate any more than the most trivial improvements in any organism.

How do I know this? Because I wrote an Ethernet book. Frameshift mutations also exist in Ethernet. They are not known to be beneficial under any circumstances. Considerable hardware and software resources are expended to prevent them. Cells likewise devote considerable resources to detecting and correcting errors.

For the creation of Nylonase, someone would have to verify their claim that there were no other kinds of mutations involved (HGT, transposition, epigenetics). None of the papers I’ve seen address this question.

To any person who is intimately familiar with digital data protocols, claims that random or frameshift mutations or copying errors cause evolution is every bit as implausible as those who say that the earth is 6000 years old.

Which is to say, a person who is not familiar with digital protocols is vulnerable to being persuaded that it’s true. Just like a person who knows nothing about geology is vulnerable to being convinced the earth is young. But a person who knows these subjects intimately would never, ever believe this. Those who do are generally swayed by their philosophical biases – ultra-literal interpretation of the Bible in the case of YEC, and atheism in the case of frameshift mutations.

From Wikipedia:

Frameshift mutations frequently result in severe genetic diseases such as Tay-Sachs disease. A frameshift mutation is responsible for the disabling of the CCR5 HIV receptor and some types of familial hypercholesterolemia (Lewis, 2005, p. 227-228). Frameshift mutations have also been proposed a source of biological novelty, as with the alleged creation of nylonase. However, a study by Negoro et al (2006) [1] found that a frameshift mutation was unlikely to have been the cause and that rather a two amino acid substitution in the catalytic cleft of an ancestral esterase amplified Ald-hydrolytic activity.

patrikbeno says:

“I deny that frameshift mutations all by themselves can generate any more than the most trivial improvements in any organism.”

Perry, in pseudo-digital world of DNA there is no such thing as trivial improvement. If trivial improvement is possible, you cannot deny possibility of non-trivial ones.

Not mentioning the fact that the classification trivial / nontrivial is full of prejudice and chauvinistic anthropocentrism.

“Frameshift mutations also exist in Ethernet.”

What does not exist in Ethernet, Perry, and you know that, is sexual recombination (which boosts useful genetic variation buildup) and natural selection (which does the bullshit filtering).

Anyway:

A series of recent studies by a team led by Seiji Negoro of the University of Hyogo, Japan, suggest that in fact no frameshift mutation was involved in the evolution of the 6-aminohexanoic acid hydrolase. However, many other genes have been discovered which did evolve by gene duplication followed by a frameshift mutation affecting at least part of the gene. A 2006 study found 470 examples in humans alone.

http://www.ncbi.nlm.nih.gov/pubmed/17512009
http://tinyurl.com/384ql6z
http://www.ncbi.nlm.nih.gov/pubmed/16890400
http://tinyurl.com/2bkd6yc

But that’s just very interesting stuff, not intended to move you from your position :-P
Well, it might. But I don’t get my hopes too high :-)

Patrik,

Consider the following: Natural selection exists in every aspect of the digital world. Because computer programs are subject to replication and variation, and they are all suitable or unsuitable for some task. Every second of the day, millions of files are copied between computers on the Internet. And none of the corrupted copies are ever known to more suitable. If they were, someone would know it – and they would be taking advantage of it. But they’re not.

Stop and ask yourself why this is not happening.

There is no such thing in digital communication theory as a “percentage of time that a corrupted signal is better than the original.” The concept simply does not exist.

Ask yourself why.

There is also no such thing as a commercially available software product that was created by (a) random mutation & natural selection, or even just (b) genetic algorithms.

Ask yourself why.

“Trivial” is not a question of prejudice or anthropomorphism, it’s an issue of measurable, demonstrable functionality.

Example: A frameshift mutation could conceivably be responsible for changing

the quick brown fox jumps over the lazy dog
to
the quick brown fox jumps over the lazy doll

that’s trivial.

However there is no realistic statistical possibility for it to change it to

the quick brown fox jumps over the lazy ferret

without a series of steps in the middle, in which the word “dog” would be mis-spelled and the whole sentence would get eliminated by natural selection before it became a readable sentence. Because codes are discrete, not continuous.

The only way you can get a sentence or any kind of digital instructions to evolve is through discrete substitutions and re-arrangements of genes or parts of genes. Without modular, discrete re-arrangements you will never achieve phenotypes that survive natural selection. Not in English, not in any computer language, and not in DNA.

As for your first statement: “If trivial improvement is possible, you cannot deny possibility of non-trivial ones.”

If Darwnism was actually concerned with building a working theoretical model of evolution rather than evangelizing philosphical reductionism, you wouldn’t be saying this. Because any functional evolutionary model has to demonstrate that significant new features can develop in acceptably short periods of time.

Throwing up your hands and saying “Given enough time anything is possible” is not science. Very tiny improvements that are likely to happen one time per billion copying errors do not explain things like how Nylonase digestion occurs within a small culture of bacteria. Let alone something enormous like the Cambrian explosion. This is why Darwinists are taught to strenuously avoid any discussion of statistics or probability.

HGT, transposition, epigenetics, genome doubling and symbiogenesis are exhaustively documented, parsimonious explanations for organizational adaptation.

In contrast, nowhere in the entire body of biological literature is there a single paper that demonstrates that random mutations alone produce evolutionary changes such as the ability to digest nylonase.

If you disagree, then show me one.

My larger question for you is:

Why do you still prefer a theory of random accident when documented systematic re-arrangements are already in the literature for 50 years now?

Respectfully, Patrik, it seems to me that if you did not define yourself as an atheist, you would no longer be “required” to prefer random accident over modular re-arrangements of genes, and you would then be allowed to simply follow the evidence where it leads.

patrikbeno says:

Perry,

(Sorry for a long post again, this is sort of multi response to 2 of your comments.)

“Why do you still prefer a theory of random accident when documented systematic re-arrangements are already in the literature for 50 years now?”

That’s a huge misunderstanding.

I am not insisting on random mutations only. That would be foolish. After all, we have to explain evolution of intelligence.

== Intelligence ==

We have to explain evolution of intelligence. Intelligence did not just accidentally *pop* into existence. It evolved in gradual small steps (whatever the evolution driver was). At some point, there must have been an even a semi-intelligent bacteria (we cannot skip that step).

Hence, I am far from denying Shapiro.

Intelligence is implemented as a set of complex interactions of matter. Matter always interacts according to existing natural laws of physics/chemistry. We cannot have intelligence outside matter (we have no reason to believe it is even possible).
Interacting matter is a prerequisite. Intelligence is a consequence (maybe even inevitable but that’s nowhere near certain today).

Think for a while how intelligence actually works. It does not deny physics/chemistry. It works on top of them. It is assembled from smaller building blocks. It needs those building blocks.

Any cognitive phenotypic features needed by intelligence are implemented on top of the physics/chemistry, not aside of them.

We cannot postulate existence of non-matter based intelligence just because we see matter-based intelligence.
Also, we cannot postulate existence of non-physical world because we see physical world.

We cannot even define those terms meaningfully. What is a non-physical, non-matter based intelligence? What is a non-physical world? What the heck is a 1D cube?

By learning and training, level of intelligence can be increased. Since intelligence did not magically pop into existence, it is reasonable to assume that current level of intelligence is a product of some kind of evolution from lower levels.

So, using progressive improvements, driven by some kind of a selection pressure, intelligence may grow from simple mechanical intelligence to complex conscious intelligence (or even backwards, from smart to stupid).

[Evolution of intelligence, Sternberg&Kaufman, 2001]
[Thinking Ape: evolutionary origins of intelligence, Byrne 1995]
[Dragons of Eden, Sagan, 1986]

== Evolution ==

-> Random chance to begin with
-> simple mechanical intelligence
-> cognitive intelligence
-> learning/remembering intelligence
-> self-aware introspecting intelligence
-> consciousness
-> multigenerational continuum of memory/consciousness via memeplex inheritance

(Role of randomness in evolution decreases with increasing level of intelligence)

Ad. trivial changes and evolution:
Macroevolution is composed of microevolutionary events. Sequence of various trivial changes leads to different species in the long run. This is basically proven by common descent.
http://en.wikipedia.org/wiki/Common_descent
(Forget for now about whether these changes are designed or not, it is irrelevant. The point is that trivial changes between every step in 1..1000 accumulate to make illusion of big significant change visible when comparing the step #1 to step #1000)

Evolution is not about giant leaps and frog giving birth to dog or elephant. But you know that.

Anyway, I guess the whole history of genetic algorithms proves you wrong.
http://www.talkorigins.org/faqs/genalg/genalg.html
http://en.wikipedia.org/wiki/List_of_genetic_algorithm_applications
http://en.wikipedia.org/wiki/Computer-automated_design
http://en.wikipedia.org/wiki/Evolutionary_algorithm

Considering our hardware is nowhere near to be able to simulate nature’s parallelized computational power, I think we have quite a success with evolutionary simulation even without intelligent designer.
http://en.wikipedia.org/wiki/Tierra_(computer_simulation)
http://en.wikipedia.org/wiki/Avida
http://en.wikipedia.org/wiki/Artificial_life

== Reductionism ==

I see complex things composed entirely of simpler things. And these complex things do not violate but obey the rules and laws of the simpler things.
I see evidence for reductionism everywhere. There’s nothing wrong with this idea.

History shows that any complex feature, when finally understood and explained, it is understood and explained by decomposition to simple terms, their interactions, and rules of those interactions.

== Information ==

Information is a product of the intelligence.
Information does not exist without intelligence.
You need intelligence to create or detect/infer information.

But the whole concept of “information” is *void* without intelligence.
Information depends on interpretation.
Virtually any piece of data can become an information.
Intelligence is what gives arbitrary data structures a meaning – making it an information.

See this for fun:
http://www.bible-codes.org/index.htm#bible-code-site
and remember Skinner’s pigeons:
http://en.wikipedia.org/wiki/B._F._Skinner#Superstition_in_the_pigeon

This tells us a lot about how pattern-seeking intelligence can easily get misguided and misinterpret the information or even see one where there is none.

== Follow the Evidence ==

I already followed evidence where it leads. Away from creationism (“atheist” is just a label for non-creationist).
You think the evidence leads to creationism.
One of us is wrong, that’s all. And both of us have our biases. So let’s face them.

== Word Games ==

1. DNA is intelligent.
2. All intelligence we know the origin of, is based on DNA.
3. Therefore, we have 100% inference the designer must be DNA-based, and 0% inference that he is not.

Just saying…

patrikbeno says:

Ad. nylonase and frameshift:

there are two altered enzymes, not just one. Both these enzymes are needed to metabolize the 6-aminohexanoic-acid-cyclic-dimer (6-AHA CD) found in the waste water of the nylon factory. Neither of these enzymes alone is effective. Both are needed.

enzyme 2 is the product of a frame shift. … [snip] … it is also the product of 140 point mutations. Many of these mutations are silent, but many are not. 47 amino acids out of 392 of the enzyme have been changed.

http://aslodge.tripod.com/id89.htm

Patrik,

Is a frame shift and 140 point mutations the only change to that genome? Or were there also elements of transposition, HGT and other kinds of systematic behavior as well?

Could it be reasonable to postulate that the 140 point mutations are the result of orchestrated systematic behavior rather than random copying errors?

Is the above question in keeping with the spirit of scientific inquiry, which is to look for rules and systems?

patrikbeno says:

enzyme 1 would be product of HGT, enzyme 2 would be:

“…the product of a frame shift. … [snip] … it is also the product of 140 point mutations. Many of these mutations are silent, but many are not. 47 amino acids out of 392 of the enzyme have been changed.”

However intelligent and designed the other changes are, the depend on enzyme #2 which is a result of the frame shift.

HGT copies stuff. It does not invent it. It copies blocks.

Point mutations called “point” for a reason (point, not block). They are caused e.g. by a frame shift. A framing error. A reading frame shift. (May also be a random undirected mutation caused by external environment, a cosmic gamma rays or something, that’s hard to distinguish from copy errors when it happens.) It is something you don’t believe can be of any evolutionary significance. Something that always happens and causes mostly damage. But this time, it becomes kinda useful.

HGT is a bacterial sex. It increases the genetic variation by combining existing information. (This is why random sexual recombination is more evolutionary powerful than simple random mutation. This is why HGT is more powerful evolutionary driver that random mutation. We have mathematical models and genetic algorithm proving this.)

HGT happens even between different species of bacteria. Does this imply there is only one bacteria species? Does this imply that the design is so powerful that single bacteria species is aware of design of all other possible species? Even those not yet evolved or evolved on another continent?

HGT also causes mutations that do nothing useful (beyond increasing genetic variation), like sexual recombination does. Why is that and how does the bacteria know that this time we’re just messing with the genes and this time we’re desperately looking for a nylonase?

If this mutation would be conscious or intentional or designed or orchestrated or systematic as you are suggesting, why also silent (NOP) mutations? Why even bother? What’s the point?

Random mutations and copying errors certainly occur (let’s leave aside level of their evolutionary power for a moment). They are dangerous because they are stupid, they more easily break the design than create something useful.
And yet there are random mutations in bacteria. If bacteria are so smart, why don’t they fix all random mutations? In bifurcating reproduction model, there is a hell of a lot material to use to fix these errors.

Why is that these mutations accumulate in non-coding part of the DNA in the same frequency across the globe and across the species? Shouldn’t the higher order, more complex, more intelligent species have more intelligent DNA?

Frameshifting occurs even during protein translation, thus breaking decoder (Farabaugh, 1996) . As far as I know, correction mechanism is only available for copying sequence. There is no correction mechanism in protein translation process (decoder). What is so intelligent about that?

Scientific inquiry for rules and systems?


Is the above question in keeping with the spirit of scientific inquiry, which is to look for rules and systems? ”

In science, teleological thinking like this gets us nowhere. We can postulate designer and stop at any moment of our inquiry (which has been the case so many times in history).

Emergent systems

We are trying to explain how systems and patterns emerge. What rules are involved and why that happens. These rules are so far always a consequence of the other rules.
Every time we unwrap the layer of some complex stuff, we find something smaller and simpler and less intelligent. Every time we see that complex is more than just sum of its parts (emergent systems).
Mammals are more intelligent that plants. Plants more intelligent than bacteria. Bacteria are more intelligent than single cell. Single cell is more intelligent than DNA. DNA is more intelligent than atom. Atom is more intelligent (if I may still use the word) than its protons. Proton is more intelligent than the quarks it is composed of.
Eventually, there will be strings or something and I bet they are as dumb and purposeless as it gets. All they can do is interact somehow when they are close to each other.

Look at gravitational systems: One simple rule and what beauty, symmetry, order emerges. Almost perfect circle orbits of planets in Solar system, all oriented in the same way, all planets rotating in the same direction. Yet it is natural cause of a simple rule. Gravity.

No designer involved nor needed.

Intelligent designer theory has absolutely no explanatory power. It is just a statement of our ignorance, metaphysical “I dunno”. Its appeal is purely emotional, not intellectual. Understandable but irrelevant.

Patrik,

You asked: If this mutation would be conscious or intentional or designed or orchestrated or systematic as you are suggesting, why also silent (NOP) mutations? Why even bother? What’s the point?

Let me clarify that I’m not advocating “theistic evolution” as though God manually nudges these steps along. I’m suggesting that bacteria are cognitive and possibly even conscious and that they know what they are doing in some sense. So why might there be silent mutations? Because an organism might modify a line of code but still “comment it out” or switch off that subroutine and save it for later use. Just like you do.

You asked: “how does the bacteria know that this time we’re just messing with the genes and this time we’re desperately looking for a nylonase?”

Because the bacteria knows that the nylonase is there and that if it can figure out how to digest it, it won’t starve. Just like a human saying “There’s no cows to kill and there’s no fruits or berries but what if I eat these roots or leaves?”

You asked: “If bacteria are so smart, why don’t they fix all random mutations?”

Because they’re not smart enough to fix all of them. Any line of code can become so corrupted that it’s beyond recognition or repair. But you’re asking the wrong question. The question you should be asking is, “How is it that these tiny machines are literally smart enough to identify bad lines of code and fix them? What can I learn from these bacteria and incorporate into my own computer programs?”

I hypothesize that this frameshift mutation in concert with 140 point mutations which produced a new enzyme is not a copying error. I hypothesize that it’s systematic behavior that is not yet classified.

You said: “In science, teleological thinking like this gets us nowhere. We can postulate designer and stop at any moment of our inquiry (which has been the case so many times in history).”

So let’s look at the path of this conversation so far.

Your bias is to call these 140 point mutations random accident (which stops any further investigation). Mine is to look for a systematic mechanism.

Which view stops inquiry? Which view pushes it forward?

Earlier in this thread you started out telling me “Of course bacteria are stupid. They are not aware of the attack. They lack infrastructure for this.”

According to your accusation, teleology is a statement of our ignorance and a metaphysical ‘i dunno.’ Our discussion about teleology and my blog post and Shapiro’s amazing papers provoked you to look deeper and after some investigation you send me a link to this beautiful video by Bonnie Bassler. And all this is just the beginning of a huge rabbit hole about how cool bacteria really are.

You’re a very smart guy and you’re very well read. So I can’t help but wonder, why didn’t the atheists tell you about this stuff? Why weren’t they telling you how smart bacteria are?

You’re telling me that this new enzyme for digesting nylonase came about by accident. I’m telling you that there’s probably a mechanism whose operation can be discovered.

Which philosophical perspective, during the last 2 weeks of this conversation, has provoked more discovery? The anti-teleological view or the teleological view?

Which view is more in keeping with the spirit of science, which searches for underlying order and systematic explanations?

I agree that every time we unwrap the layer of some complex stuff, we find something smaller and simpler. I’m not sure I agree it’s always less intelligent. I don’t think we know how intelligent bacteria really are. But still I get your drift. And I am loathe to introduce a god of the gaps argument where it doesn’t belong.

But there’s another side to this.

How long have atheists passionately advocated the junk dna theory? 30 years now? I wish I had a dollar for every atheist who’s sent me an angry email saying “OK so if there’s a design at work, then why is 97% of my DNA junk? Huh? Answer me that, Perry!!!” And now it turns out the junk DNA hypothesis has been wrong all along and 90% of the DNA hasn’t even been studied yet because someone called it junk. Not only that, it’s the most interesting part of the genome. It’s where most of the evolution actually happens.

An ID person or a creationist would never propose a “junk DNA” theory.

Who’s putting forth a statement of ignorance? Who’s advocating “I dunno”?

Whose appeal is purely emotional not intellectual?

You said, “No designer involved or needed”:

You still haven’t answered any of my questions about codes and evolving codes. Where’s your example of a code that’s not designed? Where’s your example of a non-alphabet evolving into an alphabet without intelligent agency? Where’s your example of no linguistic rules evolving into language and instructions without intelligent agency?

Patrik,

First of all let me congratulate you on being one of the few who approach this argument in a smart way. You’ve made some excellent points. I’m glad you’re here. I think this will be a productive conversation.

Naked facts:

1) If we temporarily set aside evidence for experiences of spiritual beings, miracles etc, then you’re right, in the scientific laboratory we do not have direct observation of non-physical intelligence.

2) In the scientific laboratory we also do not have direct observation of intelligence or codes arising purely from matter.

What a perfect “setup”! Given those two facts it’s perfectly understandable why some people see the world as top-down (metaphysics first) and others see it as bottom up (reductionism).

I think it is no more reasonable to forbid the concept of intelligence outside of matter than it is to forbid the concept of intelligence coming from matter. We do not seem to have direct evidence for either. Shouldn’t we be allowed to ask both questions?

So why do I say that we do in fact have reliable scientific inference to non-physical intelligence and zero inference to intelligence arising from non-intelligence?

Because of how information is encoded and decoded. In engineering speak, because of the OSI 7 Layer Model, which reflects how all types of information are built.

Information is always encoded top-down and always decoded bottom-up. So far as I’ve seen, there are no exceptions to this.

You write text in English. You paste it into a 1 page MS WORD document. It is encoded into Microsoft’s format and saved as a 1-dimensional string of 1′s and 0′s. You send that document to me by encoding it into an email MIME message which is then encoded into TCP/IP which is then encoded into an Ethernet packet which is then encoded into bits on a wire.

The person at the other end uses the exact reverse process to decode it:

Bits on a wire > Ethernet
Ethernet > TCP/IP
TCP/IP > MIME
MIME > MS WORD
MS WORD > your original text in English
your original text in English > Understood by person who can read English

As you probably know I’ve skipped a couple of layers, and as you probably know, each of these encodings is extremely complex and multi-layered itself.

So your document is like a nested set of Russian dolls. A message within a message within a message.

So what happens when you try to evolve that MS WORD document with point mutations of the digital file?

You could try point mutations of the document file itself, as it is written on your hard drive.

You could try point mutations in the TCP/IP encoded version.

You could try point mutations in the Ethernet encoded version.

I encourage you to try this experiment yourself.

If you have all the supercomputers in the world at your disposal, doing RM+NS for you, can you get your Word doc to evolve any greater measurable fitness for any given purpose in any less than literally trillions of years?

By all means, I encourage you to go ahead and test it and report your results.

As a communications engineer I predict the experiment will fail. The only way you will get your message inside your WORD document to evolve is for a person or software program that understands English to change the text according to the spelling and grammatical rules of English, inside a MS WORD Editor.

Any other way of modifying it shatters the entire data structure, corrupts the file and makes it unreadable.

This is true regardless of whether the application layer program is MS Word, or Excel, or an Oracle database, or a compiled computer program in any known language.

In order for something to evolve, the evolutionary mechanism has to obey the rules of the code. And there’s a different set of rules for every single layer of code.

In OSI the layers are:

Application
Presentation
Session
Transport
Network
Data Link
Physical

In linguistics the layers are

Pragmatics
Semantics
Syntax
Statistics

Both models are saying the same thing:

Information always begins with intent which is encoded into meaning which is encoded into grammatical structures which are encoded into words which are encoded into letters.

The exact reverse procedure is performed when interpreting the message.

So: Information creation is always top-down, not bottom up.

APPLICATION: Can you show any real-world example where the following happens:

-> Random chance to begin with
-> simple mechanical intelligence
-> cognitive intelligence

-Can you show any real-world example where non-alphabetic non-characters evolved into an alphabet and characters without the help of outside intelligence?

-Can you show any real-world example where alphabetic characters evolved into words without the help of outside intelligence?

-Can you show any real-world example where words assembled into proper grammatic structures without the help of outside intelligence?

-Can you show any real-world example where grammatic arrangements of words evolved into meaningful statements without the help of outside intelligence?

-Can you show any of these things happening in any sphere of the scientifically testable world? (English, Chinese, computer programs, music, CAD files, etc.)

I invite you to point to any empirical example.

To date I have never encountered any. That is why my thesis is that biological evolution likewise is top-down, not bottom up. It is directed by the agency of the cell and its built-in linguistic tools, not by random outside forces.

Genetic algorithms only work to the extent that they incorporate some level of top-down judgment to guide their behavior. Yes, I am well aware of programs like Avida etc. But their actual use in the real world is surprisingly limited – they’re mostly used as a last resort. They’re ridiculously clumsy compared to human programmers. If a programmer writes buggy code, a GA cannot fix it without a lot of help from a human. There’s no software program you can buy anywhere that was written exclusively by a genetic algorithm.

And GA’s only work to the extent that they “Cheat.” None of the GA’s that actually work authentically mimic Neo-Darwinian random mutation and natural selection. All of them hold certain parts of the data constant while mutating others; all of them are pre-programmed with a certain level of “forgiveness” in the natural selection process so that they can successfully “climb Mount Improbable” without falling into crevices.

Therefore I do not see GA’s as being successful examples of blind evolution. I see them as highly inefficient engines of design.

In order for code to exist, the rules of the code have to exist first.

And the rules of any code are immaterial. In an actual working system, the rules themselves are implied, not explicitly stated. A computer keyboard that converts keystrokes to ASCII may not have the rules of ASCII explicitly stated anywhere physically. However those rules can be directly inferred from its behavior.

What is implied / inferred is that the table existed before the keyboard was built.

The same is true of the genetic code.

I know of lots of empirically demonstrable evolutionary processes that occur once codes and instructions are in place.

I do not know of any empirically demonstrable random evolutionary process, in any context or system, that has been shown to generate codes, without intelligence.

Therefore we have 100% inference that codes have to exist first before evolution can take place. Therefore we have valid inference based on all known facts that the genetic code existed before the cell did.

My challenge to you is to name any counterexamples to what I have just said.

Consider this:

What if, instead of bringing a reductionistic bias to the question, you took a neutral position?

What if you said, “There may be both bottom-up and top-down forces at work here” ?

What kind of additional hypotheses about evolution might you entertain if you’re willing to consider that there’s more at work here than reductionism?

Is there any reason why hypothesizing a top-down program is contrary to the scientific method?

As a programmer, what if you asked, “How many of the following mechanisms might I find examples of, already in DNA?”

Error correction
Redundancy
Checksums
Arbitration mechanisms
Objects
Subroutines
Hardware
Software
Application layer programs
Data collision resolution mechanisms
Data packets
Databases
Communication protocols
Data repair mechanisms
Ports
Sockets
Diagnostic tools
Compilers
Debuggers
Modular code

As a programmer, what if you ask, “How many of these functions are carried out more elegantly in DNA than they are in man-made programs?”

As a programmer, what if you ask, “Do I have hard evidence that undirected random mutation and natural selection actually produce any of these structures?”

patrikbeno says:

Perry,

2) In the scientific laboratory we also do not have direct observation of intelligence or codes arising purely from matter.

We don’t need it. We have direct observation that intelligence and codes need matter to function. Hence there is a strong evidence to support the matter->intelligence causal link.

What a perfect “setup”! Given those two facts it’s perfectly understandable why some people see the world as top-down (metaphysics first) and others see it as bottom up (reductionism).

I agree it is “understandable why some people prefer metaphysics” but for a completely different (mostly psychological) reasons.

On factual level, I don’t agree. There is a lot of evidence to support reductionism. If there is any evidence to support metaphysics (and I am not aware of any), still the amount of evidence is significantly greater in favor of reductionism.

I think it is no more reasonable to forbid the concept of intelligence outside of matter than it is to forbid the concept of intelligence coming from matter. We do not seem to have direct evidence for either. Shouldn’t we be allowed to ask both questions?

Of course we are allowed to ask both questions. In fact, we should.
But I hope I explained to you that both world views cannot be simultaneously true and the evidence , while not 100% conclusive, is much stronger in support of reductionism.

Patrick,

“We don’t need it?”

You’re kidding. We don’t need evidence?

OK, so you say you’ve got a scientific theory – and you don’t even have inference, let alone evidence. But you’re telling me your theory doesn’t even need empirical support?

On what basis do you let yourself off of that hook? We’re talking about science here, aren’t we? Or are we just going to practice philosophy and throw out the scientific evidence?

You’re telling me there’s more evidence for reductionism and in the same breath you’re telling me no evidence is needed.

Yes, I fully understand that intelligence and codes need matter to function. Software needs hardware. But the hardware does not write the software. Ever.

I submit to you that every bit of your professional experience and actual working knowledge supports the teleological thesis and not the materialistic thesis.

I re-state my original thesis:

1. The pattern in DNA is a code.
2. All codes we know the origin of are designed.
3. Therefore we have 100% inference that DNA is designed and 0% inference that it is not.

The evidence, while not 100% conclusive, is much stronger in support of teleology.

joe says:

Quote: “When people say “genetic code” they talk about a correspondence between DNA/mRNA and the proteins (amino acid sequences) they give rise to in living cells. It’s just an observation of reality, which we choose to label “code”.”

I don’t understand what you mean here? The same can be said about Morse code

have at look at http://sandwalk.blogspot.com/2007/02/real-genetic-code.html it has a good review about the Genetic Code.

Quote: “This is the same procedure that we use to translate a string of dots and dashes sent over a telegraph line. The string of dots and dashes is the message, the Morse Code is the lookup table that we use to decode the message. We do not say that the string of dots and dashes is the Morse Code. We say that it’s a message encrypted using the Morse Code. Similarly, we do not say that a string of nucleotides is the genetic code. It’s the message that’s translated using the Genetic Code.” – from the above link

The Genetic Code looks like a real code to me, and most of the science texts agree its a real type of code, as the above example points out.

The Genetic Code was deciphered in 1961, just like the Enigma machine codes were deciphered during WW1 and WW2. these are just an observation of reality, which we choose to label “codes” from the above how is one a real code and the other not a real code from our “observation of reality” ?

Quote: “If by “code” you mean something with purpose, then you need to demonstrate this. Labeling reality doesn’t get you near to demonstrating facts.

I will try….
the Morse Code for …. — .-. … . gives us horse, the Morse Code for …. ..- — .- -. / — .- .-.. . gives us human male not human female the Morse code for – .-. . . gives us tree not starfish.

The Genetic Code for a horse gives us a horse, the Genetic Code for a human male will give us a human male not a human female, The Genetic Code for a tree will not give us a Starfish,Thus the Genetic Code dose serve a purpose.

Please explain how the Genetic Code is not a code because I cant see your point of view where its not a real type of code, I seem be misunderstanding the point you are trying make. Cheers :)

PS how do you format your text in the posts ??

Old Git Tom says:

Joe,

yes, the genetic code & morse code are the same in this respect; they are combinations of media & messages. Neither works without some form of intelligence. I can send a morse message in the medium of a sequence of dots & dashes. Unless some intelligent receiver has the necessary skill/knowledge, s/he cannot decode that message, atho can receive unintelligible dots & dashes.

So the problem explained by Perry Marshall; where or what is the intelligence that encodes a set of instructions in DNA, in the medium of amino acids? What intelligence decodes it? All other coding forms we know of demand the input of intelligence. OGT

Thanks Tom. And Joe, just to clarify, I’m not saying that ribosomes have to be intelligent to decode amino acids into proteins. Rather, what I am saying is that this decoding obeys the rules of a very rich and complex language and the origin of any language demands explanation. Everything we know about linguistics, digital communication and computer science tells us that only intelligent sentient beings create languages.

patrikbeno says:

Perry, I really enjoyed this TED talk and I am sure you are gonna enjoy it as well:

http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html

Just… Fascinating.

Now the creepy thought: How is that the very same information given in this talk will result in completely opposite understanding and conclusions?

Doesn’t that reveal something about the information theory and communication systems? It looks like different decoders can provide different, even contradictory information, no matter what the encoder puts in. Looks like receiver endpoint (interpretation) is way more powerful than the whole preceding communication system infrastructure :-)

(I hope to reply to your previous comments soon… Why’s ‘reply’ link missing?)

Patrik,

Reply link: WordPress only nests so many comments. You may have to start a new thread at the bottom of the page.

Awesome video.

I’m not sure this video provokes opposite understandings – not of what’s going on at least. My thesis from the beginning of this article was that bacteria are literally smart enough to evolve and they do it purposefully. Great soundbytes from Dr. Bassler:

“This is the word that it talks with” – molecules

“Exquisite specificity in these languages for intraspecies communication”

“Bacterial Esperanto”

Initiate pathogenicity via quorum sensing

Bacteria talk to each other

Bacteria are multi-cellular

Can distinguish self from other – “By using these two molecules they can say me and they can say you.”

Develop strategies to impede/improve quorum sensing

“Extremely complicated chemical lexicon”

“In the spirit of TED they are doing things together because it makes a difference.”

“You’ve evolved a few bells and whistles but all of the ideas are in these simple systems that we can study.”

Yes indeed, notice all the encoder and decoders, and how molecules are manufactured and every single atom becomes the letter of an intricate language. Mind-blowing.

By the way isn’t it interesting how… teleological bacteria’s behavior is? One is tempted to think that they’re almost like little tiny people.

kamod says:

Hello everybody,
Nice being here and with all the educated gurus with all the big English guns , I have one simple question, How come chickens, cats, dogs, and humans have stopped mutating all of a sudden? I thought since Darwin claimed we mutate, mutation should continue. Like dogs turning into lions chickens flying higher than eagles kind off. The same bacteria yesterday the same bacteria today the same bacteria tomorrow. Perry, you can say all you like but some are destined to doom and no amount of prove will change their view, well for the few that will see sense keep it up. In Nigerian we have a saying: the headstrong fly goes into the grave with the corpse.

patrikbeno says:

kamod,

You are wrong. Mutation did not stop. This is why e.g. our current antibiotics are about to become useless – viruses mutated and developed resistance to our “weapons”.

There are many other examples of mutation. Also many laboratory experiments observing mutation.

Google is your friend.

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