# Aphrodite’s head: Eight questions for Douglas Axe

Over at Evolution News, Dr. Douglas Axe argues that merely by using very simple math, we can be absolutely certain that life was designed: it’s an inescapable conclusion. To illustrate his case, he uses the example of a rugged block of marble being transformed by natural weather processes into a statue of a human being. Everyone would agree that this simply can’t happen. And our conclusion wouldn’t change, even if we (i) generously allowed lots and lots of time for the statue to form; (ii) let each body part have a (discrete or continuous) range of permitted forms, or shapes, instead of just one permitted shape; (iii) relaxed the requirement that all body parts have to form simultaneously or in sync, and allowed the different parts of the statue to form at their own different rates; and (iv) removed the requirement that the different parts have to each form independently of one another, and allowed the formation of one part of the statue to influence that of another part.

In his post, Axe rhetorically asks: if we’re so sure that a rugged block of marble could never be transformed by the weather into a human statue, then aren’t we equally entitled to conclude that “blind natural causes” could never have “converted primitive bacterial life into oaks and ostriches and orangutans”? In each case, argues Axe, the underlying logic is the same: when calculating the probability of a scenario which requires many unlikely things to happen, small fractions multiplied by the dozens always result in exceedingly small fractions, and an event which is fantastically improbable can safely be regarded as physically impossible.

In an attempt to persuade Dr. Axe that his logic is faulty on several grounds, I’d like to put eight questions to Dr. Axe, and I sincerely hope that he will be gracious enough to reply.

My first question relates to the size and age of the universe. As I understand it, Dr. Axe, you define “fantastically improbable” as follows: something which is so improbable that its realization can only be expected to occur in a universe which is much bigger (or much older) than our own. Indeed, on page 282 of your book, Undeniable, you further stipulate that “fantastically improbable” refers to any probability that falls below 1 in 10116, which you calculate to be the maximal number of atomic-scale physical events that could have occurred during the 14-billion-year history of the universe. You calculation requires a knowledge of the age of the universe (14 billion years), the amount of time it takes for light to traverse the width of an atom, and the number of atoms in the universe. So here’s my first question for Dr. Axe: how is the design intuition supposed to work for an ordinary layperson who knows none of these things? Such a person will have no idea whether to set the bar at one in a million, one in a billion, one in 10116 , or even one in (10116)116. I should also point out that the figure you use for the number of atoms in the universe refers only to the observable universe. Astronomers still don’t know whether the size of the universe as a whole is finite or infinite.  And it gets worse if we go back a few decades, in the history of astronomy. Until the 1960s, the Steady State Theory of the universe was a viable option, and many astronomers believed the universe to be infinitely old. How would you have argued for the design intuition back then?

My second question relates to functional coherence. You make a big deal of this in your book, Undeniable, where you managed to distill the case for Intelligent Design into a single sentence: “Functional coherence makes accidental invention fantastically improbable and hence physically impossible” (p. 160), where functional coherence is defined as a hierarchical arrangement of parts contributing in a coordinated way to the production of a high-level function (p. 144). The problem with your statue illustration should now be apparent. A statue has no functions. It just sits there. Consequently, whatever grounds we may have for rejecting the supposition that ordinary meteorological processes could transform a block of marble into a statue, they obviously have nothing to do with the argument you develop in your book, relating to functional coherence and whether living things could possibly be the product of unguided natural processes. So my question is: will you concede that the marble block is a bad illustration for your argument relating to functional coherence?

My third question relates to the identity of the object undergoing transformation. In your statue illustration, you ask whether “a rugged outcrop of marble would have to be altered by weather in only a few reasonably probable respects in order to convert it into a sculpted masterpiece.” Obviously, the answer is no: the number of steps would be extremely large, and the steps involved would be fantastically improbable. You then compare this case with the evolutionary claim that “blind natural causes converted primitive bacterial life into oaks and ostriches and orangutans.” But there is an obvious difference in the second case: the primordial bacterium itself is not being changed into an orangutan. Its very distant embryonic descendant, living about four billion years later, is developing into an orangutan. Its ancestors 20 million years ago were not yet orangutans. Self-replication, along with rare copying mistakes (mutations), is required in order for evolution to work. So I’d like to ask: why do you think it’s valid to infer from the fact that A’s changing into B is a fantastically improbable event, that A’s distant descendants gradually mutating into B is also fantastically improbable?

My fifth question relates to thermodynamics. I’d like you to have a look at the head of Aphrodite, below (image courtesy of Eric Gaba), known as the Kaufmann head. It’s made of coarse-grained marble from Asia Minor, and it dates back to about 150 B.C.

You’ll notice that her face has worn away quite a bit, thanks to the natural weather processes of weathering and erosion. This is hardly surprising: indeed, one might see weathering and erosion as an everyday manifestation of the Second Law of Thermodynamics: in an isolated system, concentrated energy disperses over time. Living things possess an unusual ability to locally decrease entropy within their
highly organized bodies as they continually build and maintain them, while at the same time increasing the entropy of their surroundings by expending energy, some of which is converted into heat. In so doing, they also increase the total entropy of the universe. But the point I want to make here is that a living thing’s highly useful ability to locally decrease entropy is one which a block of marble lacks: its thermodynamic properties are very different. So my question to you is: why would you even attempt to draw an inference about the transformations which living things are capable of over time, based on your observations of what happens to blocks of marble? And why would you encourage others to do the same?

My sixth question relates to your probability calculations. In your post, you explain the reasoning you employ, in order to justify a design inference: “it takes only a modest list of modestly improbable requirements for success to be beyond the reach of chance.” You continue: “Once again, the reasoning here is that small fractions multiplied by the dozens always result in exceedingly small fractions.” Now, this kind of reasoning makes perfect sense, if we are talking about dozens of improbable independent events: all you need to do is multiply the probability of each event, in order to obtain the probability of the combination of events. But if the events are not independent, then you cannot proceed in this fashion. Putting it mathematically: let us consider two events, A and B. If these events are independent, then P(AB) is equal to P(A) times P(B), and if both individual probabilities are low, then we can infer that P(AB) will be very low: one in a million time one in a million equals one in a trillion, for instance. But if A and B are inter-dependent, then all we can say about P(AB) is that it is equal to P(A) times P(B|A), and the latter probability may not be low at all. Consequently, in an inter-dependent system comprising dozens of events, we should not simply multiply the small probability of each event in order to compute the combined probability of all the events occurring together. That would be unduly pessimistic. And yet in your post, you attempt to do just that, despite your earlier statement: “Do I assume each aspect [of the statue] is strictly independent of the others in its formation? No.” So I’d like to ask: if you’re willing to grant that the even the formation of one aspect of a statue may depend on the formation of other aspects, thereby invalidating the method of calculating the probability of the forming the whole statue by multiplying dozens of “small fractions,” then why do you apply this invalid methodology to the formation of living things?

My seventh question relates to the vast number of possible pathways leading to the formation of a particular kind of living thing (such as an orangutan) from a primordial ancestor, and the even vaster number of possible pathways leading to the formation of some kind of living thing from the primordial ancestor. The point I want to make here is a simple one: this or that evolutionary pathway leading to an orangutan may be vanishingly improbable, yet if we consider the vast ensemble of possible pathways leading to an orangutan, the probability of at least one of them being traversed may not be so improbable. And even if we were to agree (for argument’s sake) that the likelihood of an orangutan evolving from the primordial ancestor is vanishingly low, when we consider the potentially infinite variety of all possible life-forms, the likelihood of evolutionary processes hitting on one or more of these life-forms may turn out to be quite high. It is this likelihood which one would need to calculate, in order to discredit the notion that all life on earth is the product of unguided evolutionary processes. Calculating this likelihood, however, is bound to be a very tricky process, and I doubt whether there’s a scientist alive today who’d have even the remotest idea of how to perform such a calculation. So my question is: what makes you think that an untutored layperson, with no training in probability theory, is up to the task? And if the average layperson isn’t up to it, then why should they trust their intuition that organisms were designed?

My eighth and final question relates to algorithms. Scientific observation tells us that every living thing, without exception, is put together by some kind of biological algorithm: a sequence of steps leading to the formation of an individual of this or that species. The algorithm can thus be viewed as a kind of recipe. (Contrast this with your illustration of a statue being formed by blind meteorological processes, which bears little or no relevance to the way in which a living thing is generated: obviously, there’s no recipe in the wind and the rain; nor is there any in the block of marble.) In order for “blind natural processes” (as you call them) to transform a bacterial ancestor into an orangutan, the algorithm (or recipe) for making an ancient bacterial life-form needs to be modified, over the course of time, into an recipe for making an orangutan. Can that happen?

At first blush, it appears fantastically unlikely, for two reasons. First, one might argue that any significant alteration of a recipe would result in an unstable hodgepodge that’s “neither fish nor fowl” as the saying goes – in other words, a non-viable life-form. However, this intuition rests on a false equivalence between human recipes and biological recipes: while the former are composed of letters which need to be arranged into meaningful words, whose sequence of words has to conform to the rules of syntax, as well as making sense at the semantic level, so that it is able to express a meaningful proposition, the recipes found in living things aren’t put together in this fashion. Living things are made of molecules, not words. What bio-molecules have to do is fit together well and react in the appropriate way, under the appropriate circumstances. Living things don’t have to mean anything; they simply have to function. Consequently, the recipes which generate living things are capable of a high degree of modification, so long as the ensembles they produce are still able to function as organisms. (An additional reason why the recipes found in living things can withstand substantial modification is that the DNA found in living organisms contains a high degree of built-in redundancy.)

Second, it might be argued that since the number of steps required to transform a bacterial ancestor into an orangutan would be very large, the probability of nature successfully completing such a transformation would have to be fantastically low: something could easily go wrong along the way. But while the emergence of an orangutan would doubtless appear vanishingly improbable to a hypothetical observer from Alpha Centauri visiting Earth four billion years ago, it might not seem at all improbable, if the Alpha Centaurian also knew exactly what kinds of environmental changes would befall the Earth over the next four billion years. The probability of evolution traversing the path that leads to orangutans might then appear quite high, notwithstanding the billions of steps involved, given a suitably complete background knowledge of the transformations that the Earth itself would undergo during that period. In reality, however, such a computation will never be technically feasible: firstly, because we’d probably need a computer bigger than the cosmos to perform the calculation; and second, because we’ll never have the detailed knowledge of Earth’s geological history that would be required to do such a calculation. So my concluding question to you is: given that the probability of nature generating an orangutan from a bacterial ancestor over a four-billion-year time period is radically uncomputable, why should we trust any intuitive estimate of the probability which is based on nothing more than someone eyeballing a present-day bacterium and a present-day orangutan?

Over to you, Dr. Axe. Cheers.

## 311 thoughts on “Aphrodite’s head: Eight questions for Douglas Axe”

1. Entropy,
You give colewd too much credit. When he writes of “50% substitutability”, he means that, at every position, there are only 10/20 amino acids that will provide minimal function. This is clear from his use of 50%^L for the proportion of sequence space that is functional. Put another way, he is claiming that, for any of his proteins of interest, fully 50% of its nearest neighbors in aa sequence space are without selectable function. This is demonstrably wrong. (I pointed him to McLaughlin et al. Nature 491, p138 (2012), without effect.)

2. This is demonstrably wrong. (I pointed him to McLaughlin et al. Nature 491, p138 (2012), without effect.)

I will take a longer look at this. Happy New Year Jock 🙂

3. Entropy: Yes, they can (hell, yes!).

That’s literally what some times leads to amyloids. Repating CAG expansions for example create beta sheets, which can stack and fold into amyloids.

Beta-propeller domains emerge from beta sheet repeat motifs.

Some of the oldest protein folds in existence, such as ferredoxins are hypothesized to have begun as repeating the same small mineral cofactor-binding motif over and over again. And so on and so forth.

4. Entropy: Yes, they can (hell, yes!).

That’s literally what some times leads to amyloids. Repating CAG expansions for example create beta sheets, which can stack and fold into amyloids.

Beta-propeller domains emerge from beta sheet repeat motifs.

Some of the oldest protein folds in existence, such as ferredoxins are hypothesized to have begun as repeating the same small mineral cofactor-binding motif over and over again. And so on and so forth.

I’d like to second Entropy in thanking Rumraket for providing this info 🙂

Below are some excerpts from Rumraket’s link.

Using alternative repeat domains for specific protein binding may allow optimization of the biophysical properties of protein scaffolds

The wisdom of nature. As Goethe said, “Eternally she creates new forms. What now is, never was in time past; what has been, cometh not again – all is new, and yet always it is the old.”

The authors of the piece speculate on the evolution of protein domain repeats:

A likely scenario, is that repeat proteins expand rapidly until a physical/structural limit has been reached and subsequently diverge rapidly since repeat domains tend to only have weak sequence similarity[38]. One possible explanation for their propensity is that their structures allow expansion and, additionally, may provide novel ligand binding…

Particularly higher eukaryotes are prone to rapid repeat expansion[39][40], as is immediately obvious from the abundance of repeats in eukaryotic genomes compared to prokaryotic.

This rapid expansion followed by diversification of protein repeats reminds me of the path of development of cells from an individual zygote. Protein repeats are just one example of nature using the repetition of form. Other examples are segmented body plans, the vertebrate spinal column, cell division, leaves along a stem, convergent evolution of bodily forms. This truth is captured by a phrase I think is worth pondering over, “as above, so below”.

Here is what wikipedia says about amyloids:

Although bona fide amyloid structures always are based on intermolecular β-sheets, different types of “higher order” tertiary folds have been observed or proposed. The β-sheets may form a β-sandwich, or a β-solenoid which may be either β-helix or β-roll. One complicating factor in studies of amyloidogenic polypeptides is that identical polypeptides can fold into multiple distinct amyloid conformations.[4] This phenomenon is typically described as amyloid polymorphism. It has notable biological consequences given that it is thought to explain the prion strain phenomenon, for example.

If identical polypeptides are able to fold into multiple conformations, then how is the folding controlled? The control cannot originate in its amino acid sequence.

One way of analysing proteins is to crystalise them in order to determine their shape. But in so doing the essential nature of many protein complexes is lost. To give an analogy, our hands have a specific shape, but it is the dynamic way that our hands can be used that makes them such special structures. It is the dynamic way that complexes such as molten globules and amyloids can be used that allows them to function as they do.

Living forms are not created by DNA. Organisms use their DNA to produce the polypeptides required for their growth and in order to function.

5. Alan Fox:
Spider silk

Spider silk

Spider silk is known for its exceptional toughness and flexibility. It is several times stronger than steel, and yet is much more flexible. As a result, efforts are being made by scientists around the world to try to develop analogues that could be used in industrial and medical applications. However, though it is known that the beta-sheets in spider silk are key to its strength, how the sheets are formed is poorly understood, making it difficult to create artificial variants. Part of the reason it is difficult to understand the mechanism is that the silk is initially created as soluble proteins, which very quickly crystalize into a solid form, and it has been very difficult to analyze the soluble form…
Essentially, their studies demonstrated that the polyproline type II helix can form a rigid structure which can then be transformed into beta-sheets very quickly, allowing the silk to be quickly woven. Intriguingly, it turned out that pH — which is thought to be important for the molecular interactions of the N- and C-terminal domains — does not play an important part of the folding of the repetitive domains, and that it is rather the removal of water and mechanical forces as the precursor moves through the silk gland.

A good example of how organisms use their polypeptides.

6. Probabilities, Charlie, I was referring to those probability calculations that you were hinting in your previous post. I asked you a very straightforward question, what are you calculating the probability of and why are those functional constraints relevant to that probabilistic model? Billy loves to assume equiprobability of all sequences, so his calculation ends up modeling a stupid tornado-in-a-junkyard scenario that no one believes in. Can you do a little better? I mean the bar is pretty damn low

IMO statistics are too easily manipulated into saying whatever one wants them to say. I leave that to others who have an interest in that sort of thing.

But I do know that no amount of time would be enough to allow weathering to transform any sort of natural rock into a form as distinctly carved by an intelligent being as is Aphrodites head.

I’m not sure what the image of stones provided by Rumraket here is trying to prove. All that it demonstrates is that humans can design objects which range in appearance from amiguously designed to obviously designed.

I first saw the structure in the image below when I was a young child. At a distance it looks quite impressive from one angle but as you travel further along the road it is apparent that the impression isn’t consistent. And even as a young child I could see that it was just a natural formation in the rock.

7. CharlieM: A good example of how organisms use their polypeptides.

Without even knowing what polypeptides are.

Of course.

How many people use silicon chips without even knowing what they are? I would hope we all know that practical use and knowledge are two different things. We do not have to know how a phone works in order to use it.

8. CharlieM: IMO statistics are too easily manipulated into saying whatever one wants them to say. I leave that to others who have an interest in that sort of thing.

LMAO. So now you want to skip all talk about probabilities, so you can fall back to your intuitions. Okay

CharlieM: But I do know that no amount of time would be enough to allow weathering to transform any sort of natural rock into a form as distinctly carved by an intelligent being as is Aphrodites head.

Who the fuck cares? What does that have to do with anything, in particular, the proteins we were discussing?

CharlieM: I’m not sure what the image of stones provided by Rumraket here is trying to prove. All that it demonstrates is that humans can design objects which range in appearance from amiguously designed to obviously designed.

No, it’s just to point out that you have no rigorous design detection criteria. Just a bunch of worthless intuitions. Sure, we can build (the fuck with that design BS) stuff that resembles other stuff, and nature can build stuff that resembles faces and statues.

Yawn.

My point was, stop talking about probability if you have no idea what you’re calculating the probability of. You know what’s ironic? If you don’t lay out exactly the process / event for which you’re calculating it’s probability, then it’s you who’s torturing statistics by pulling stats out of your ass to have them say whatever you want them too.

Now you want to avoid using the term probabilities, and apparently you also want to stop talking about proteins. You’re back to your irrelevant analogies and intuitions about statues. Whatever Charlie, whatever

9. CharlieM: Without even knowing what polypeptides are.

Of course.

How many people use silicon chips without even knowing what they are?

The vast majority

I would hope we all know that practical use and knowledge are two different things. We do not have to know how a phone works in order to use it.

Agree, but you still need to know something about a phone to use it.

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