@dsterncardinale
This comment seems to have been orphaned in the thread split, and I’m not sure where it belongs.
That is a response to this comment.
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Why would you have moved a post that starts with:
“I think Douglas Axe did a pretty good job calculating the probability of a single protein forming naturally…”
And it was 2004, not 2003.
Because it was the start of the off-topic wander. If necessary, quote the relevant part of the comment and bring it back here.
Thanks for the correction, I will edit.
We know a being created them, and that’s the point, the who, when or how might not be known to know that. You’ve made my point for me.
Right, but that is the point of Dr. Axe’s research: the improbability of even the simplest functional protein forming by unguided chance. His work calculated that the likelihood of a random sequence folding into a stable, useful configuration; something that can actually perform a biological function, is astronomically small. The analogy to dice is apt: a fair die landing on six occasionally tells us nothing, but if it lands on six a hundred times in a row, chance is no longer a reasonable explanation. Axe showed that the search space for proteins is so vast, and the functional islands so vanishingly rare, that the repeated “successes” we see in biology cannot plausibly be the result of blind sampling. It implies the presence of direction—of design.
rather than posting your entire section, I’ll post the conclusion.
The biological world demonstrates a continual preferential sorting that works to protect information from corruption. Mutation, the supposed engine of change, is overwhelmingly destructive. Studies in population genetics show that detrimental mutations outnumber beneficial ones by at least a thousand to one, and often by as much as a million to one (Eyre-Walker & Keightley 2007; Elena et al. 1998; Loewe & Hill 2010). Life endures only because it preserves its information through intricate repair and error-correction systems that guard the message with astonishing fidelity. These mechanisms succeed with remarkable consistency, maintaining functional integrity across generations. When they fail, most changes are absorbed or corrected before they can spread, and the few that persist typically reduce function or terminate viability. The purpose is unmistakable: the system exists to prevent change, not to invite it.
Any mechanism that exhibits preference for one state over another, accurate sequence over random mutation, cannot arise from a mindless mechanical system, for in a mindless, preference-less universe, there is literally no necessary difference between the two states. Physical law operates by necessity, and probability operates by chance; neither possesses the capacity to value one sequence over another. Preference is the defining mark of intelligence, the power to discern and assess one state from another. That is why an archaeologist can distinguish an arrowhead from a chipped stone with complete confidence, why you can confidently say the Statues on Easter Island are manmade. The shape alone reveals preference, and the specified order, it’s purpose.
What evolutionary theory quietly smuggles in is the presupposition of survival as a given. It treats the drive to survive as an inherent property of living systems, when in truth it is nothing of the sort. Matter has no concern for its persistence. A computer does not care whether its circuits are functioning; but I do. The tendency toward self-preservation is not built into the material; it is an expression of preference, and preference belongs to mind.
Because survival is so pervasive in biology, specifically in our own experience, its presence is taken for granted. It has become invisible to those who study it. Yet its ubiquity does not make it natural; it makes it extraordinary. Physical law has no capacity for concern, no internal rule that declares existence preferable to nonexistence. The fact that every living system behaves as though it values its own continuation is therefore not an outcome of physics, but evidence of intention impressed upon the physical system. Survival is not a given of nature; it is the signature of design. Without it, “fitness” has no meaning, no power, and no point.
If we concluded the statues were made by rabbits, or by leprechauns, that would be ridiculous. Rabbits don’t build things, and leprechauns are mythological. Likewise, concluding a Designer with no a priori evidence the the Designer’s existence is simply concluding a tacit assumption of the person reaching that conclusion.
Got to call you on this, three or four times times even.
- β-lactamase is not a simple protein, as I’m sure our biochemists will confirm.
His work calculated that the likelihood of a random sequence folding into a stable, useful configuration; something that can actually perform a biological function, is astronomically small.
- As already noted by @Nesslig20 above, even simple sequences can have function.
2.5) That astronomically small probability is considerably larger if we incorporate any amount of selection for fitness. It also doesn’t mean anything until we have a comparable probability for Design, which we don’t, because there is no Design hypotheses that can do that (Ewert’s maybe, but it remains to be done).
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Nowhere in all of the biological sciences will you find a claim that proteins originate from randomly assembled nucleotide.
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Axe extrapolates from a single complex protein that ALL proteins must be difficult to evolve (a hasty generalization). Most proteins are part of larger families of functional proteins, which are variations of a basic template. (But I’m the statistician, I’ll let the people who know speak to that in more detail.)
Simply not true. MORE descendants survive because of these repair mechanisms, which is good for overall fitness. The biological world does indeed “demonstrate a continual preferential sorting that works to protect information from corruption”, AND we see this is the number of failed reproduction attempts, the number of extinct species. In other words, the biological world is expending energy - and expelling corrupt information - to maintain and possibly improve information related to fitness in the environment.
Fibonacci sequences, Fractals, Spirals, Symmetry, Tessellations, Meanders, Waves, bubbles and foams, cracks, spots and stripes, crystals, “Normal” curves (and other statistical distributions). I surely missed a few.
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And he got it wrong. His experiments can’t tell us that because they are incorrectly designed to get at that question. Further still, even supposing (against actual evidence) his number is even close to correct, that still tells us nothing about whether new proteins can evolve, or how beta-lactamase came to exist, because we know it evolved from related proteins.
He did not show that at all. His experimental method can not support that conclusion.
Does truth matter to you or are you merely here to just assert these falsehoods for appearance’s sake?
There are some competent molecular biologists around who are familiar with his paper and his work, and I happen to know quite a bit about that particular subject myself. I invite you to take a look at Axe’s methods in detail, so that we can discuss them here.
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Have you heard of the concept of an attractor?
I’m sorry but your posts read like you’ve got all your education from reading only creationistic sources, and you know next to nothing about the real sciences of biology, chemistry, or physics.
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Bad example. We know exactly who created them, and when, and how. Your point is unmade.
You clearly have no idea how natural selection works. Organisms that don’t reproduce don’t contribute to the next generation. Organisms that don’t perform behaviors that lead to reproduction don’t contribute to modern populations. There’s the reason modern organisms exist instead of not existing.
Exactly. It’s an outcome of natural selection.
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Have they exhibited the intellectual capacity for such things, yet rabbits make homes, and runs, more examples of intelligent design. Now, your postulation of a Leprechaun is curious, we have about as much evidence it could make those statues as we do for unguided nature, perhaps more… who knows what forms of intelligent life preexisted our records.
As you pointed out, we both agree unguided nature a laughable assumption, and I agree… thus we both appeal to Intelligent design is the last and only serious theory standing.
Invoking “selection for fitness” does not solve the problem of probability. It only hides it. Fitness is an arbitrary criterion that relies on a hard wired preference to survive. Without that preference, all bio mechanical systems would fail. Molecules do not seek persistence, and cells have no concern for their own continuation. The tendency toward survival is not a necessary property of matter; it is a value embedded in the system itself.
When fitness is used as an explanatory mechanism, it smuggles in that same unacknowledged preference. Nature has no capacity to favor one configuration of molecules over another, yet the language of “selection for fitness” assumes such favor at every step. It is a metaphor borrowed from intelligence and imposed on matter. The invocation of fitness does not remove the need for design; it depends on it.
Ok, lets drill into Dr Axe’s research:
When we ask how likely it is for a functional protein such as β-lactamase to arise without any preexisting informational or cellular framework, we are not asking about variation within life. We are asking about proteins in general, using β-lactamase as a clear and measurable test case. Life depends on thousands of proteins with precisely defined shapes and functions, each essential to cell structure and metabolism. β-lactamase simply lets us see, in practical terms, what kind of probability space we are dealing with.
The enzyme Axe studied contains about 150 amino acids. Each position in that chain can be one of 20 possible amino acids, giving a total of 20¹⁵⁰, or roughly 10¹⁹⁵ possible sequences. That number defines the size of the search space, a space so vast that it cannot be explored by any conceivable physical process in the known universe.
Axe’s experiments measured how many of those sequences produce a stable, functional fold. The result was about one in 10⁷⁷. In other words, for every working enzyme, there are one hundred trillion trillion trillion trillion trillion trillion trillion failures. To grasp the scale: if every atom in the Milky Way were a random protein factory producing a new sequence every microsecond since the Big Bang, we still would not expect to stumble upon even one functional enzyme by chance.
Most random chains of amino acids do not fold at all. They collapse into useless tangles or disintegrate as unstable fragments. The specific folding pattern that gives a protein its function depends on precisely arranged chemical properties — polarity, charge, and hydrophobic pairing — distributed across the entire length of the molecule. That pattern is like the etched circuitry of a microprocessor: every connection must be positioned in exact relation to every other for the entire device to operate.
A functional protein, like a processor, is not defined by its raw material but by the organization impressed upon it. The logic of the fold determines how it channels energy and carries out instructions, much as transistor pathways determine how a chip processes information. Molecular chaperones that guide and protect folding serve a role similar to thermal control and error-checking systems in electronics — preventing overloads, stabilizing structure, and ensuring reliable operation.
Both systems require foresight and precise constraint. The microprocessor does not emerge from random etching on silicon, and a functional enzyme does not emerge from random chains of amino acids. In both cases, what makes them work is not the material itself, but the encoded relationships between parts — the architecture of information that gives matter its purpose.
So when we ask how many possible folds would have to be attempted to achieve that specific shape, the answer is on the order of 10⁷⁷ failed attempts for every one success. And β-lactamase is only one example; the same improbability applies to the vast array of essential proteins needed for any viable cell. Without a preexisting informational system — no translation machinery, no quality control, no molecular chaperones — even a single working sequence would have no context to reproduce or persist.
The conclusion is unavoidable: from a standing start, random chemistry cannot reasonably produce a functional protein. The existence of even one fold like β-lactamase, let alone the full suite of enzymes required for life, points not to the power of accident but to the presence of design impressed upon matter from the beginning.
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It does because instead of selecting for a specific structure-function relationship (e.g. proteins with the “beta-lactamase fold”), we’re selecting for any fitness enhancing function.
Since we’re discussing the evolutionary origin of functional proteins, there’s nothing arbitrary about using fitness as the criterion. It is, after all, the fitness-effects of mutations that determine their probability of being passed on to the next generation.
In collection, some sets of molecules do. Those are known as dynamic attractors, and living cells are an example.
Sure it does. It favors configurations where opposite charged particles are attracted to each other. Crystal formation and growth is a concrete example of a specific configuration being favored over innumerable other possible arrangements of the same atoms.
Why are you so fantastically wrong about everything you say? All your posts read like you’ve only ever got your education from reading creationist material, or old books about vitalism from the 1800’s.
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Even William Dembski knows better than that,
It really isn’t. It’s based on the actual ability to produce offspring that survive to adulthood.
But - with the correct understanding of fitness - this is not true. Those best equipped to produce offspring that survive to adulthood will - on average - succeed more often at doing so and so contribute more to the next breeding generation. If the traits that make them fitter are heritable, these, too will be more frequent in that generation as a consequence. Selection is a natural consequence of fitness.
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Yes let’s do that. I suggest we begin by looking at his experimental methods.
Only if we do that can we determine whether he can extract the conclusion he does from his experimental results.
Methods.
That isn’t a question Axe asks anywhere in his paper. If you disagree please quote the part of his paper you think supports that inference.
No. Axe’s paper is about TEM1 beta-lactamase only and exclusively, not any and all proteins in general. And it’s not about the origin of life, or the origin of proteins “without any preexisting informational or cellular framework.”
Really? How did he do that?
Please explain his methods in your own words. Tell us how these measurements were made.
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Seems like some bait and switch here. Concluding that humans create carved statues based on our existing knowledge of humans and human abilities to carve statues is not something we necessarily call “intelligent design”. I would call it “human manufacture “.
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Then it’s utter nonsense that he went backwards, beginning with an already unstable temperature-sensitive (ts) mutant and changing 10 residues at once, no?
In what way does that measure “the probability of anything forming by unguided chance”?
And why did Axe treat the continuous (over many orders of magnitude) variable as a binary one? In the context of what you wrote, wouldn’t “the simplest functional protein” be one with orders of magnitude less activity than either the wild-type or the ts mutant that he used?
No, Axe extrapolated. You’re misrepresenting what happened.
There are many things wrong with your claim.
- Stability is not simply a good thing.
a) Making proteins more stable is fatal in many diseases (prions, diabetes, etc.).
b) Axe didn’t bother to measure stability. Why are you bringing it up as though he did? - Axe’s binary assay is not an accurate measurement of enzymatic function; I suspect that this was by design. Or he did the measurements and omitted the data.
a) There are simple kits for measuring beta-lactamase activity.
b) Please explain why you think Axe didn’t use them. - What is your prediction of the frequency at which one would find by screening short, 110-residue variable regions of immunoglobulin genes for beta-lactamase activity?
- If this was so groundbreaking, why didn’t Axe follow it up in the last 21 years? He’s had plenty of money provided by the DI to do so.
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Re your first statement: The claim that “unguided evolutionary processes produce immense complexity” mistakes what is actually being observed. What we see are pre-loaded informational systems adapting within designed limits. Every living cell carries an operating framework capable of environmental sensing, feedback, and targeted adjustment without collapsing the larger structure. That is not blind mutation generating new order; it is a deeply resilient architecture expressing built-in adaptability.
The very fact that organisms can undergo such change without disintegrating under the weight of random variation is itself astonishing. Designing a system with that level of malleability—able to adjust to shifting conditions while preserving core function—would be an engineering achievement beyond anything humans have yet built. The observation does not support unguided complexity; it demonstrates the foresight of a system built to evolve without destroying itself.
Also, our observation is that all beings capable of intelligent design only come into existence thru the DNA system. So, the most logical conclusion, following your reasoning, is that the DNA system could not have been created by an intelligent being.
I chose this statement because it repeats one of the most common and mistaken forms of reasoning used against design. It’s the same pattern seen in the watch-on-the-seashore example: we find a watch, recognize purposeful construction, and infer intelligence. The rebuttal then tries to short-circuit the reasoning by saying, “Yes, but because we know humans make watches that’s a good inference, but there were no humans hundreds of millions of years ago to make life; therefore Intelligent Design necessarily is ruled out.”
That move is fallacious. It shifts the question from “Is this the kind of thing that shows design?” to “Did a human make it?” and then declares the inference to ID invalid simply because a human candidate is absent. In so doing, it confuses the recognition of design with the identification of the designer. This is not reasoning; it is a categorical dodge that bypasses the very question under discussion.
- Category Error
A mistake of mixing distinct kinds or levels of explanation.
It occurs when someone treats a property that belongs to one class of thing as though it belongs to another.
Example: claiming that “evolution produces information,” when evolution operates within an informational system but does not generate the system itself. That is like saying gravity “builds bridges” because bridges obey gravity. - Circular Reasoning (Begging the Question)
Assuming the very thing one is trying to prove.
The conclusion is embedded in the premise, usually disguised by rephrasing.
Example: “All intelligence arises from DNA-based organisms, therefore intelligence cannot precede life.” The statement only works if one has already assumed what it claims to demonstrate. - False Equivalence
Treating two unlike things as though they are identical because they share one superficial trait.
Example: “All intelligent beings we know are biological, therefore intelligence requires biology.” That is as mistaken as saying “All known books are made of paper, therefore words cannot exist without trees.” - Straw Man
Misrepresenting an argument to make it easier to defeat.
Example: saying “Design theor claims God built every species separately,” when the actual claim concerns the informational origin of life’s systems, not the sequence of creation events. - Ad Hoc Explanation
Adding an extra assumption solely to rescue a failing theory.
Example: “If evolution cannot explain a feature, perhaps we simply haven’t discovered the mechanism yet.” This introduces an unfalsifiable escape clause rather than evidence. - Non Sequitur
A conclusion that does not logically follow from the premises.
Example: “Life evolved from nonlife, therefore purpose is an illusion.” Even if one accepted evolution, it does not follow that life is purposeless. - False Cause (Post Hoc)
Assuming that because one thing follows another, it must have been caused by it.
Example: “Because complexity increased after natural selection began, selection created complexity.” Correlation does not prove causation. - Argument from Ignorance
Claiming something must be true because it has not been proven false, or vice versa.
Example: “We don’t have direct evidence of designer, therefore we can ignore ID as an option.” Ignorance of evidence is not evidence of absence. - Equivocation
Using the same word with different meanings within an argument, creating the illusion of agreement or proof where none exists.
Example: conflating thermodynamic entropy (a measure of energy dispersal) with Shannon entropy (a measure of information uncertainty), and then treating them as interchangeable. The argument “open systems can decrease entropy and therefore increase information” commits this fallacy. A local thermodynamic decrease does not create new informational order; it merely allows it to exist if an informational system already directs it. This shift in definition hides the core issue behind verbal similarity. - Composition and Division
Assuming what is true of the parts must be true of the whole, or vice versa.
Example: “Mutations can change genes; therefore, mutation can invent entirely new systems.” What is true of small variations is not automatically true of integrated complexity. - False Dilemma
Presenting two options as the only possibilities when others exist.
Example: “Either evolution explains everything or you believe in magic.” This excludes the third option — that intelligence operates through law. - Appeal to Authority
Citing expertise as proof rather than evidence.
Example: “Most scientists accept common descent, therefore it must be true.” Authority can inform, but it cannot substitute for argument or data. - Naturalistic Fallacy
Assuming that whatever is natural must therefore be the origin or standard of what ought to be.
Example: “Because nature shows competition, morality must arise from selfishness.” It confuses description with justification. - Self-Refuting Claim
A statement that undermines itself by its own logic.
Example: “There is no truth.” If that were true, the statement would also be false. Similarly, “Reason is a product of blind chance” nullifies its own authority. - Category Closure (Question Dismissal)
Declaring a topic meaningless because it falls outside one’s chosen framework.
Example: “The origin of information isn’t a scientific question.” That is not a rebuttal but a refusal to engage the question itself.
The cited natural patterns; fractals, spirals, and crystal lattices, are products of necessity, not preference. They arise from mathematical and physical constraint, where behavior follows deterministically from initial conditions. Water flows downhill because gravity requires it. Such regularities are a result of the necessity of natural law, not choice.
Preference represents the ability of a system to evaluate alternatives and act contrary to default gradients when a particular outcome is valued. This distinction defines the boundary between necessity and preference: law constrains behavior to a single outcome, whereas intelligence, and machines they create, deliberate in the determination of the best option that fulfills its Preferential value structure.
The hallmark of intelligence is its capacity to act against entropy. All unguided systems tend toward equilibrium—energy disperses, gradients flatten, and information decays through noise. Intelligent activity reverses that drift. It concentrates energy, maintains gradients, repairs damage, and preserves coded relationships that would otherwise erode.
Physical law can generate structure, but only intelligence can sustain organized complexity against continual thermodynamic and informational decline. The persistence of low-entropy states through feedback, repair, and error correction therefore constitutes the operational signature of design. In physical terms, intelligence is the sole known process that persistently drives matter and information counter to the universal gradient of entropy.
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