Intelligent Design on Trial

Faith & Science Conversation
74

When Nobel laureate Marshal Nirenberg set out to break the genetic code, he did not use a mathematical formulation to calculate the end results of his research. Instead, he used an isolated translation apparatus taken from an existing cell. He then manipulated the input into the system and documented the output. What he documented at the output could never be derived from the input, even in principle. There is a physicochemical discontinuity between them.

The relationships between input and output had to be demonstrated by Nirenberg because they cannot be derived through formulas. This is what physicists call a “non-integrable constraint”, because there is no rate expression to integrate into a complete description. Yet, you seem to be asking for a mathematical formula to demonstrate that CTA represents leucine, and that CAG represents glutamine, otherwise apparently, genetic translation is not science. Just how much of biology do you want to do away with?

[quote=“Nuno, post:70, topic:3710”]
As I mentioned above, no one disputes that there is organization in the cell and in living systems. [/quote]

The issue is not that there is organization in living things; the issue is the material conditions required for one thing to represent another thing in a material universe (where nothing represents anything else). In order to organize the cell, physical objects (such as the amino acids used to create proteins) must be individually specified among alternatives and placed under temporal control. It is the organization of this capacity that is the issue.

[quote=“Nuno, post:70, topic:3710”]
what we cannot agree on is that the existence of living cells (and thus “the capacity to encode memory using dimensional representations”) just by itself is “proof” of intelligent agency. [/quote]

I don’t see the need in blurring important distinctions. We do not infer intelligence from the existence of a living cell “just by itself”. We draw a valid inference from the fact that the unique physical conditions of language use can be positively identified among all other physical systems, and that these exact conditions are demonstrated by the translation of genetic information.

Also, I’d like to comment on your repeated use of the word “proof” as the thing ID must provide. I assume you know that science is not in the business of providing “proof” of theories. Scientific measurements can only disprove theories, or be consistent with them. In this instance, it is our universal experience that intelligence is required to organize the unique physical conditions of language (i.e. the capacity to encode and translate spatially-oriented representations, along with establishing the constraints of a reading frame code). In stark contrast to this, there isn’t a shred of empirical evidence that the physical conditions of language rise from electromagnetism and gravity acting on inanimate matter. The claim that intelligence is required for the physical conditions of language is singularly consistent with the physical evidence. All other claims are therefore inconsistent with that evidence. This is the reality of the matter. There is no scientific justification to avoid it.

And finally, let us just take your objection at its core claim – we cannot agree that the capacity to record and translate language provides “proof” of intelligence. Just allow that roll around a minute.

Let us now re-tune your objection to reflect the actual situation – we cannot agree that the capacity to record and translate language infers the presence of intelligence.

What is interesting is the belief you are eager to place in front of this inference. It is a theory without an equivalent empirical support; one that can never be tested, but is readily defended by the mere assumption of its truth, against universal evidence to the contrary? And yet at the same time, don’t your comments reflect the general idea that I (as your conversation partner) am not meeting your standards of reason?

Please tell me something: What is the mathematical proof of biogenesis without intelligence? And should we apply your same standards here, as you apply them to ID? If you are unable to provide what you demand from ID, aren’t your beliefs and objections tied to a theory that’s not science?

Somehow, I suspect not.

[quote=“Nuno, post:70, topic:3710”]
I already agreed above that your model can be used to represent the basic arrangement of information in cells insofar as it captures their genome/proteome/organism structure. [/quote]

The model describes the material conditions required to translate information into physical effects.

[quote=“Nuno, post:70, topic:3710”]
I would not necessarily go as far as asserting it’s “required” in the sense that “there can be no other way to transfer information” but that is probably not relevant to the point you’re trying to make. [/quote]

If the genetic code-word (codon) for leucine is transcribed and presented to the ribosome, then leucine will be presented for binding to a new protein. If the codon is not presented, then leucine will not be presented for binding.

Now scrape that whole system off, and imagine how you might accomplish the task. You’re going to need a medium to specify leucine and its alternatives. But nothing inherently specifies anything else, so you cant rely on the physical properties of the medium to do the specification.

The actual cell, of course, uses one arrangement of matter to act as a representation, and another arrangement to establish what is being represented. It’s able to function because the organization of the system preserves the natural discontinuity between the medium and its effect.

But what will you do?
.

With that, I think we’ve taken this exchange as far as we can. I’ll resist the urge to summarize. My time is becoming limited, but we can continue if you think there is anything left.

75

Tony, thank you for the reply. I will have to circle back to post a follow-up.

76

@Biosemiosis.org

There are some points that I would like to clarify.

It is important to understand that a mathematical formulation (end even proofs) do no have to actually use “formulas” in an algebraic sense. For example, mathematical formulations of classical computer science problems are often specified as optimization problems on graphs (e.g., the Travelling Salesman Problem). The word formulation indicates a requirement for a formal specification but that does not have to be an actual formula.

That said, the answer to your specific question is that the mathematical formulation and “proof” for the anti-codon / amino acid relationship is the structure of tRNA along with the experimentally testable model for how it is processed in the cell to translate mRNA into protein sequences. And since we’re addressing the translational processes in the cell, let me also address your other comment related to this:

I would learn a bit more about nature and realize that processes have already been discovered where large protein complexes (Non-Ribosomal Peptide Synthetases, or NRPSs for short) can directly assemble new peptides (same as proteins but shorter) without any need for mRNA templates. And since the structure of the peptides assembled by NRPSs is completely determined by the structure of the protein domains as organized in the NRPS’s three dimensional structure, it would seem that their existence would falsify your claim that “nothing inherently specifies anything else, so you cant rely on the physical properties of the medium to do the specification.”

This is a good example of why I find it careless to claim that “there can be no other way” to do things simply because we have access to a very common way of doing that same thing. It is also why formal proofs of impossibility are required when anyone attempts to make the extraordinary claim that “there can be no other way”.

There is no mathematical proof for biogenesis of any kind, with or without intelligence. That is why the right position is to abstain from claiming scientific proofs of biogenesis. And thus, yes, I want to apply the same standards to ID and ask that its proponents stop labeling it as a science or stop claiming to be able to demonstrate how biogenesis happened.

77

I will show you intelligent design, a women’s body is intelligently designed to carry and have a baby! she goes through lots of changes to be able to do this one thing! A man’s body however is NOT designed to have a baby or carry one!{he does NOT have the correct body parts}! Now if that is not intelligent design,I do NOT know what is! what could you say to possibly argue with this well known FACT? Not much!

78

However when you can prove evolution is true science and NOT just the “religion” of the doubters of God then I will believe it! you have failed to do that so far however!

79

@martin

I doubt you will ever find a Christian that doubts that God is intelligent or that God created (and thus designed) all that ever was, is and will be - we all agree on that. But why would anyone’s faith be compromised if we don’t call that “science”?

4 Likes
80

So what should we think about male nipples? And it’s rare, but men can even get breast cancer!

81

Good grief Nuno. You’d think from your response that I had claimed it impossible to bind one amino acid to another amino acid outside the ribosome.

You’ve put up a non-transcribable catalytic templating process as a counter-example to a genuine translation system using a set of spatially-oriented representations and a reading frame code. The problem is that these are not merely dissimilar systems; one process is an entirely different physical process than the other. The product of templating is wholly determined (and therefore limited) by the three-dimensional structure of the template, while the product of translation is determined solely by the structure of the “interpreting” arrangements (i.e. the set of aaRS) which are absolutely inert to the translation process.

You also have a certain habit of assigning to me things I did not say, and blurring the things I do say. You then characterize these things as careless. I am certainly as capable of making mistakes as anyone else, but I don’t think you will find me careless, Nuno. I do not equivocate on what it means for a representation to actually be a representation, or what it means for a representation to be translated by an inert intermediary. I do not equivocate on the enormous distinctions between a system that is entirely limited by local dynamics, and those that do not have that limitation. It has a massive effect on both sides of the cut. And on neither side of the cut, does a templating system do what a translational system does.

Your counter example falsifies nothing about translation.

It’s also important to understand that we do science in order to create formulations. Such formulations are not a bullwhip to define doing science when we don’t like the observations

The anti-codon/amino acid relationship is not established by the structure of the tRNA. That relationship is established by the aminoacyl-tRNA synthetase (aaRS).

I didn’t claim to have “mathematical proof” of biogenesis. I claimed that identifying the singular physical conditions of language and mathematics is a valid inference to the presence of an intelligence. You denied that inference on the basis that ID is not science because it does not provide a mathematical proof of how biogenesis occurred three and a half billion years into the unobservable past. But this is not a genuine demand – you don’t apply it evenly.

You seem to have lost your place here. The question was not whether you would apply your idiosyncratic standards to ID; that had already been demonstrated. The question is whether or not you apply them elsewhere without reservation. The unambiguous answer to that question is “no”. For the ideas you personally believe in, they clearly needn’t provide you proofs to win your favor, and they needn’t be re-labeled non-science until they do. This has been the problem with your position from the start. It’s not genuine. It’s a means to dismiss physical evidence.

82

@Biosemiosis.org

We may indeed have come to a point in the conversation where there may not be much of a productive way forward. But even if this is as far as it goes, I still thank you for sharing your views. We may not agree on several aspects of your approach but I certainly acknowledge it is an honest take on the concepts of IC/ID and it was useful, at least for me, to consider that approach to this question.

I hesitate to get into a “he said / he said” type of exchange but I’ll give it a try, just in case it might get the conversation back on track.

It was never my intention to falsify anything about translation (not even clear what that would mean). Let us remember how this sub-conversation came about. Your text starting with “If the genetic code-word […]” came in response to my statement that “I would not necessarily go as far as asserting it’s “required” in the sense that “there can be no other way to transfer information””. In response to that, you wrote “Now scrape that whole system off, and imagine how you might accomplish the task.”, which I took to mean “how would you construct proteins without the ribosomal translational machinery?” Thus my response that NRPSs can do that just fine.

Second, what seems falsified to me is not translation as a process but your statement that “nothing inherently specifies anything else, so you cant rely on the physical properties of the medium to do the specification.” - do you disagree that a) the three-dimensional structure of NRPSs “inherently specifies” the structure of their assembled substrates or that b) bacteria “rely on the physical properties” of NRPSs “to do the specification” of the resulting molecules? If you disagree that NRPSs falsify this statement then it would be useful to see just how so.

I agree that collecting observations is how fields of study proceed towards constructing scientific formulations but I wouldn’t necessarily call it “science” until predictive models begin to be proposed that a) can explain the observed data and b) can be falsified by new observations. Do you have any examples of fields of study that are generally recognized as “science” yet offer no formulations nor predictive models with falsifiable predictions?

If you refer to the portion of my sentence that follows right after your truncated quote of what I wrote, you will see that it also said “along with the experimentally testable model for how it is processed in the cell to translate mRNA into protein sequences.” - the model obviously includes all the enzymes and supporting structures in the ribosomal translational machinery so it’s not clear what your point was here.

Again it seems like the history of the conversation was somehow lost here - what I wrote was in response to your question: “Please tell me something: What is the mathematical proof of biogenesis without intelligence?”. You had also mentioned that “If you are unable to provide what you demand from ID, aren’t your beliefs and objections tied to a theory that’s not science?”, so I responded that I don’t know of any scientific explanation for biogenesis and thus those are the same standards I apply to ID, as I do to everything else.

This is nearly correct. A more complete statement would be “ID is not science because a) it does not provide a mathematical proof of how biogenesis occurred three and a half billion years into the unobservable past (positive proof) nor b) provide a mathematical proof that intervention by an intelligent agent is the only possible explanation for biogenesis (negative proof).” You claim that these are not criteria that I apply evenly - can you give a specific example of how that is the case?

83

I too very much appreciate your time and input into the dialogue. Thank you, Nuno.

I would only add that there is very likely no way to ever provide a “positive proof” for a one-time event in the deep unobservable past. And there is certainly no way to provide a “negative proof”. Chance is non-falsifiable on this issue.

With that being the case, I hope you might reconsider your (repeated) dismissals of the design inference on the grounds that it does not provide these forever unavailable proofs. It raises questions when you dismiss universal observations in the physics of semiosis as ‘non-science’, while merely characterizing other ideas (those you personally believe in) as “theories in the making”. In the end, these labels do nothing to benefit our understanding of physical evidence.

On Biosemiosis.org, I commend people to learn what they can of the physical evidence, to be disciplined about what can and cannot be said of that evidence, and to be fair about it.

Science cannot answer the ultimate questions of reality

The creation of space and time at the origin of the universe is an event forever hidden in the deep unobservable past. We are likely to never know, with any objective certainty, what the source of this event was. The same is true of the origin of life, the rise of consciousness, and the basis of free will. While it is entirely normal that we would want conclusive answers to these great questions, what we are actually left with is simply existence as we find it. From that, we can pursue discoveries with passion, and hope to have the wisdom to understand what the universe is telling us.

Consequently, the constant implication (by many popularizers of science) that science has answered these questions (or is on the verge of answering these questions) is unethical and cavalier with regard to the evidence. The impetus for this cavalier conduct is highly questionable, particularly given the fact that the output of this conduct isn’t an advancement on a cure for cancer or cleaner air over our cities – which are the actual hopes and dreams of the public who pays for science – but is most often social, political, and even legal in nature.

As it turns out, the greatest consequence of these questions is how we as groups and individuals choose to treat each other. This fact only underscores the necessity that we understand the limits of our knowledge, and call upon ourselves to respect rationality and intellectual freedom among all people.

Again, thank you Nuno.

84

@Biosemiosis.org

Biogenesis is an open question that I don’t follow too closely but I do seem to have higher hopes of future developments than you do. I can see how positive evidence might arise where chemical processes are found that could yield self-replicating structures with the potential to be precursors to primordial biological organization. On the negative proof side, it is indeed difficult to show that something cannot happen at all (there are only a few notorious exceptions to this) but it is often possible to show probabilistically that something is extremely unlikely to happen given only a limited set of possible operations (e.g., combinatorial chemistry)

When it comes to “theories in the making”, I had also mentioned in response to GJDS that the distinction I make is that a scientific theory should at least have some formal models with falsifiable predictions that have been corroborated by experimental observations. This is already true for many evolutionary models of smaller-scale biological organization, even if there are gaps that are still the focus of very active research.

Thank you again for our exchange may God bless you and yours in 2016 and beyond.

85

Science = this:: man discovering that which God has created! that is all science is! Nothing More or nothing less! Evolution is NOT science it is a man made idea that people use to “run from God the creator” and just make a claim that God did NOT create man!

86

@martin

Man has been misusing every type of knowledge ever since we had access to any knowledge that we could misuse - all the way from knowing about the existence of the tree of knowledge of good and evil, through melting gold into a golden calf right after all of God’s miracles in rescuing the Hebrews to today’s misuse of political power, money, looks and yes, science. The problem is not the tool, medium or type of knowledge - the problem is in the sinful nature of those who use it to go against the teaching of Jesus Christ. It’s not science itself that needs fighting against, it’s its misuse for the wrong claims or purposes.

87

@Nuno

I am all for models since I have made extensive use of QM molecular modelling in my work for many years. However, it is necessary to point out that mathematical formulations and the rigorous scrutiny needed of these is critical to the utility of any scientific modelling. In this context, natural selection (NS) takes the form of a foundation for all biologically relevant models that are considered to be based on neo-Darwinian (ND) thinking. I think the lack of any rigorous mathematical foundations for NS is more then a gap, or something that is a work in progress, but more of a fundamental flaw in ND.

To use the somewhat extreme views by some proponents of ND, who claim a similarity with QM, this is equivalent to saying we do not have the wave equation, but nonetheless QM is shown to be true by some simple models. If viewed in this (perhaps humorous) way, we would have serious doubts of ND. My personal view is that ND is a primitive, semantic notion that needs to be freed from ideological (and odd theologies) baggage, and eventually be replaced, as an inadequate outlook, by a mathematically based theory or theories of the biological disciplines. I quickly admit that such a breakthrough would take enormous effort, because the biological sciences eventually take us to perhaps some of the most difficult areas of all science. But when we mix up ND and Christian theology, these concerns on ND become valid (I assume ID stays clear of theological teachings, or at least Eddie seems to argue in this way)…

Extending our arguments to the origins of life takes us to extreme speculation, and as the reference you provide states, a lot of wishful thinking. I guess my comments would not please proponents of ND or ID :sunglasses:.

88

I agree:) that is something we can agree on!

1 Like
89

Did the judge in Dover make Intelligent Design swear to tell the truth and nothing be the truth? What did Intelligent Design say? I really truly like to know. Perhaps Patrick knows the answer. :laughing:

90

Henry,

The Judge determined that Intelligent Design is a RELIGIOUS exploration of nature … not a scientific one… because it presumes that there things that science will never explain.

While this is not technically incorrect (from a BioLogos viewpoint) … if it is RELIGIOUS … it isn’t allowed.
I believe even BioLogos accepts and promotes that position. BioLogos does not lobby school committees to have the idea that God GUIDED evolution taught in the classroom.

George

91

Have a Happy New Year!

92

@GJDS

This is an interesting question so let’s explore it a bit further.

First, it is important to define what is actually meant by the terms NeoDarwinism (ND) and Natural Selection (NS). Let’s say we start with some very simple (and admittedly incomplete) definitions of ND in the sense of genomic mutations being the means by which genomes are transformed (not just single nucleotide polymorphisms) and NS in the sense that the “fittest genomes” increase their relative proportion within the genomic diversity of a given species. Both of these can be modeled mathematically, at least in some instances. For example, BioLogos’s nice series on Lenski’s E.Coli Long Term Evolution Experiment (LTEE) is a great example where a) the genomic changes are know and can be modeled as mathematical transformations on nucleotide strings; b) the corresponding phenotypic gains in fitness can be measured because the function of the gene is known and the organism is available for measurements and c) the resulting reproductive fitness and fixation of the mutations can be measured by the increasing dominance of the genotype in LTEE’s controlled environment over a number of generations.

Now let’s say we wanted to go beyond just using this specific observation as evidence for the ND/NS hypothesis and we wanted to model the whole process mathematically. First we would need to model the different types of operations that can transform the genome and assign them probabilities according to their frequency in the LTEE environment (this would be a stochastic model, in the sense of our previous exchanges on randomness). Exhaustively exploring the space of all possible genomes resulting from just K<10 genome transformations may be borderline feasible for E.Coli on a supercomputer with enough memory, but let’s say we would model it using MCMC if exhaustive search is not feasible.

This would leave us with at least two challenges: a) how to model the phenotypic fitness of each possible genotype and b) determining how genotypic fitness (e.g., more efficient processing of a certain type of nutrient or resistance to given pathogen) translates into reproductive fitness. Neither of these is immediately obvious but the lack of an exhaustive genotype/phenotype mapping alone is reason enough why this type of model cannot progress very far at this stage of our biological knowledge.

So should we abandon the whole approach just because we cannot provide such comprehensive models today? I would argue we should not - if for no other reason, at least because we can very likely already train Markov Models on genomic transformations such that the observed outcomes would “emerge” with very high probabilities. It doesn’t yet make much sense to do that because a) the models would overfit the data given the large number of parameters and the (comparatively) small amount of data available to train them and b) the models would require gross genotype/phenotype “predictions” where current knowledge is lacking. However, what these models would show (and many biology papers show on a smaller scale) is that the ND transformations operating in NS environments do suffice to explain/support evolution on a smaller scale.

Now you might have been referring to ND/NS at a macro-evolution scale of animal and human evolution, in which case the models above are definitely way too simplistic to describe those systems. But given the history of this thread and the question’s focus on mathematical models, it seemed appropriate to at least consider how these models could be constructed at today’s more tractable scale.

93

Have a Happy New Year!