What did the first functional cell look like and how do you know this?
The inference isn’t drawn from purpose, especially since purpose can be unknown or transient. Generally we infer manufactured objects through recognition of form.
I’m cases where recognition of form can be ambiguous, we may look for specific hallmarks of manufacture, such as in the case of distinguishing stone tools from naturally occurring rocks.
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The bacterial flagellum does not display coding or error correction. It’s components are encoded in DNA, it does not itself encode anything.
In every other known case, the designer is humans.
In every known case of a designer (including humans), it is one that itself evolved and must have gone through a process of learning how to design and construct things by interacting with the environment, taking in chemical energy (or in the case of photosynthesis, radiation), and expending it on the process of cogitaiton, learning, designing, and manufacturing it’s designs, and through that creates heat (thereby increasing the total entropy of the system).
This is just fantastically wrong. All designers obey the laws of thermodynamics, and no known designer can create information (or anything else) without expending energy and creating heat in the process.
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I have to say, it is very hard to believe you are acting in good faith when you continue to parrot Axe as an authority when it has already been demonstrated, not only that his paper (taken at face value) did not support the conclusion he drew from it, but that he deliberately manipulated his experimental design to produce his desired result. That is to say, he is both incompetent and dishonest. Which, of course, makes him the perfect candidate for a chair at BIOLA.
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Whoa there cowboy! 
Shannon Information is not Functional Information, however you define functional information.
Creating and preserving Shannon Information is analogous to a thermodynamic system, except there is no Second Law of Information Theory. There are several Information Inequality which are roughly similar to 2LoT, but none of these prohibit information from being preserved or new information added. The way this works is also analogous: First new (random) information is added to a population, then some of that information is discarded (not random).
It is not disingenuous, it is science. We appeal to human manufacture because we know humans exist and make things. If we appealed to aliens from Alpha Centauri manufacturing artifacts THAT would be disingenuous, because we have no a priori evidence that such aliens exist. Likewise, ID has no a priori evidence that a Designer exists.
This repeats a point I made before the thread split.
You misunderstand - Far from dismissing Ewert’s work, I think it is the greatest thing in all of ID literature, because it is the only example that comes close to stating a testable hypothesis.
AND because it is testable, it can be compared to hypotheses from evolution such as Common Descent. To my knowledge there has published a test of the Dependency Graph versus Common Descent using phylogenetic data, but the methods for doing so are well accepted. An ID research could use mainstream methods to test ID hypotheses, and there would be no arguments about the validity of methods made up from scratch (Like Dembski’s CSI). Someone could actually test ID hypotheses in the same manner as Theobald, White, and Baum.
THIS HAS NOT HAPPENED
It’s almost like ID researchers are afraid of putting their ideas to a real test.
Once again, archeologist infer human design. They do not infer the existence of humans.
And I lost the source comment, but Axe’s probability calculation and inference to Design makes the same error we started with - the probability of this (that) thread occurring by chance.
What is needed is a hypothesis for Design from which we might calculate a probability of Design to compare to a probability of evolution using the same data (Such ratios are at the heart of statistical inference).
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Do you agree with Stadler that there is no pattern of genomic similarity that is incompatible with a common design hypothesis?
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This seems to be a rather hostile dismissal of a valid point. The evidential base we usually use to conclude design is only partially present in living things - and I would say that the missing parts include the strongest evidence,
Which of course Is not my claim. Indeed the fact that the flagellum grows naturally would seem to rule out manufacture as a live option - whether human or not.
And, of course, this is an example of manufacture - which only goes to support my actual point.
You may find your arguments compelling but they are largely conjectural and weak. We do not have the full suite of evidence, nor do we have the same background information that we use to conclude design in more certain cases. There is no design theory to fill the gaps in our knowledge of how life began and changed over time. Given that we know that evolution-like processes can accomplish much without guidance, given the success of evolutionary theory in explaining as much as it has - it seems premature to jump to the conclusion of design.
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What is it, however, specifically, that you are asking about such things?
Sure. Wind and water will also not yield those nice and regular celestial cycles, like day and night or the seasons. Nature does not end with some arbitrarily narrow set of well-understood interactions[1]. There will be phenomena that fall outside of the scope of some “theory of wind and water”, but that does not mean that we do not have another description that adequately accounts for them, let alone that they must be brought about by some beyond-natural forces, even if we did not have a complete enough theory for them.
As it stands, and since you grant that nature could and would produce structures of more or less unbounded complexity, I return back to the question of… what the question even is. We understand that some complex structures tend to affect their environment in such a way as to produce out of the materials in it replicates of themselves, we should expect more such copies in the long run. We also understnad that if between several variants some do it quicker or more reliably than others, we should expect those variants to dominate the population in the long run. So then what about any naturally occurring structure is it that would have us “expect them to be created by somebody”? Especially when we are talking about things the artificial creation of which we have no experience with?
… and wind and water, frankly, are some of the more complicated higher order systems at that, anyway ↩︎
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You bet it is. So wrong. Good thing I wasn’t drinking anything because my spit take would have destroyed my keyboard.
@Thacker, did you somehow misstate your position? Unless the laws of thermodynamics got repealed while I wasn’t looking, I can’t make sense of your claim. Please explain.
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Actually, Axe did no such thing. While perusing research published by Axe and Ann Gauger in the ID journal Bio/Complexity, I came across an interesting table that relates to Axe (2004). In their paper entitled “Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention—Selection Itself Is Not Inventive” (Axe DD, Gauger AK (2015) BIO-Complexity 2015 (2):1–13. doi:10.5048/BIO-C.2015.2.), one of the avenues of investigation involved experiments on the evolution of ampicillin resistance in E. coli. The context was the larger consideration of whether “innovation”, such as enzyme activity, could appear and subsequently evolve toward some optimized state. In this study, Axe and Gauger compared evolutionary trajectories of two proteins derived from a TEM beta-lactamase – one variant that is likely bereft of authentic beta-lactamase activity (TEM-D), and the other a variant (basal-b) with a very weak activity. (Notably, basal-b is the “starting point” for the 2004 study in which Axe reported the rarity of functional sequences.) In Table 1 of Axe and Gauger (2015), these authors report that the lowest concentrations of ampicillin that completely inhibited growth of cells carrying the (inactive) TEM-D variant were 5-10 µg/mL, and the highest concentrations of ampicillin at which some growth was observed were 5-7 µg/mL. In Table 2 of this report, they state that the lowest concentrations of ampicillin that completely inhibited growth of cells with the (active) basal-b variant were 10-45 µg/mL and the highest concentrations of ampicillin at which some growth of cells with the basal-b variant was observed were 5-40 µg/mL. In other words, the lowest concentrations that inhibited growth of inactive and active variants had overlapping ranges (5-10 µg/mL and 10-45 µg/ml, respectively), as did the highest concentrations that permitted growth (5-7 and 5-40 µg/mL, respectively). Importantly, these concentration ranges include the concentration (10 µg/mL) Axe used in his 2004 report to differentiate active from inactive variants derived from the basal-b enzyme.
The ramification of these considerations is that the assay Axe used in the 2004 study cannot accurately distinguish between constructs (plasmids) encoding enzymes with very low activity and plasmids that encode enzymes devoid of any activity. He does not know whether variants scored as nonfunctional may actually have lower (say, 2 or 5-fold lower) activity, or for that matter that variants scored as active may actually lack authentic beta-lactamase activity. Since the purpose was to enumerate all functional variants (even those with much lower activity than the initial enzyme) as well as all non-functional variants, the fact that the assay cannot reliably discern between the “starting point” and controls with no activity (let along variants with slightly lower activity) renders the entire study meaningless. Axe’s number (1 in 10^77) is no more valid or accurate than one pulled out of a hat or otherwise entirely fabricated.
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Which they created by basically deleting most of the active site from the enzyme, rather than simply replacing residues critical to the activity.
Since many enzymes are thought to have evolved from noncatalytic ancestors that functioned as substrate binding proteins (or were active on other substrates), it’s… curious they take the approach of deletion to create a noncatalytic starting point, rather than simply replacing the Ser130 and Asn132 residues (among others)—normally critical for beta-lactamase activity—with something else.
And they don’t just delete a few residues critical to beta lactamase activity. The protein is missing 36 out of the normal 150 amino acids. One gets the sense they were afraid of even the possibility that a noncatalytic protein should evolve activity in their experiment.
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Energy flow can move matter around and even produce temporary patterns, but it doesn’t generate functional organization.The energy released in an explosion at a lumberyard can scatter wood and nails, yet it will never yield a painted, furnished house. We have no evidence whatsoever that a data-storage and replication system of comparable durability, reliability, and self-repair could ever arise by undirected physical processes. if you think we do, please provide it.
The question on the table is whether life can originate by purely unguided natural processes. You can’t use your own thesis — that it did — as evidence — that it did —. It’s like me saying, “God created man, and as evidence I point to your own existence, you do exist right? QED
Seriously?
What we’re looking for is an independent demonstration that undirected chemistry can produce a data-storage and self-replicating system. So far, there isn’t one. If you have an example, please produce it.
This is about as naked a circular argument as I’ve ever witnessed. You’re assuming that because life exists, and operates through chemistry, its origin must therefore be undirected chemistry. That’s the very point in question, is that evidenced?
The observation that life’s information is maintained by chemical mechanisms does not show that those mechanisms produced the information in the first place. Its like claiming a DVD is the author of the data it contains? Really?
Until you can empirically demonstrate an unguided process is able to generate new, functional, self-preserving code from scratch, the claim remains an unevidenced assertion, not evidence. Ask me to provide evidence for my claim “Only Intelligence can produce such a code”, and I’ll be happy to fill this forum with examples.
Will such examples be specific to biology (re: RNA/DNA) and include demonstrable mechanisms insofar as how said intelligence produces such things?
Or will said examples be mere analogies of various things not related to biology? The latter being par for the course in these discussions.
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Since “functional organization” is a pattern of matter, your claim is self-refuting. If energy flow can in fact move matter around, it logically follows it can in principle generate patterns that would correspond to “functional organization.”
At best what you could say, as you appear to have said in other posts, is that it would be unlikely for that particular pattern to form. But of course that assumes we already know all there is to know about the patterns into which “energy flows” are likely to arrange matter. Which would be a bold claim indeed.
If all there was at work in nature were explosions, that point would mean something.
You’ve already conceded that such evidence exists since it was you who wrote that “Energy flow can move matter around.”
But if us not presently having evidence for how X arose means it didn’t, then guess where that leaves your preferred supernatural explanation?
Having now dealt conclusively with that underlying non-sequitur, let us move on to the actual point of my response:
Since we don’t know how the first genetic polymers arose or replicated, I won’t bother speculating on that.
But it’s also irrelevant to your statement that I corrected. You claimed above, which I have highlighted in bold, that “there is no empirical or theoretical corollary by which energy flow alone can create or preserve functional information. In fact, all evidence indicates the opposite.”
This is what I was responding to, because that claim is empirically demonstrated to be untrue. We know, here actually by direct observation, that functional information can evolve, and since evolution as it occurs to populations of living organisms is only possible because organisms on Earth exist in a physical and chemical disequilibrium, it is in fact the case that “energy flow” can create functional information.
Ahh I see you got confused by my statement and thought I meant life’s mere existence is evidence for how it originated. No, I mean there’s actual evidence from the physical sciences that indicate that life originated by a physical-chemical process. You can click that link to get a short description of it.
If us not presently knowing or being able to demonstrate X means we should conclude X couldn’t happen, guess where that leaves the supernatural designer hypothesis?
Remember: All known designers are the product of evolution. So if what we only presently know or can demonstrate is the sword upon which we must throw ourselves, you’re in some deep water too I’m sorry to say.
Well I guess the same must be true of your preferred invisible designer acting in the ancient unobserved past then. “If you can’t demonstrate it it remains an unevidenced assertion.”
Of course, the idea that we have to demonstrate something to support it is itself a silly idea. One can of course conclude something by inferring it from a number of scattered clues. Direct demonstrations are often unnecessary.
You, as someone who believes something to be true we find in an old book, none of which you can repeat, observe, or demonstrate, you presumably still believe there are good reasons to believe what the book says. Right? You infer, from these reasons, that the events and so on described in the book really happened, despite not having observed or demonstrated any of them. As such you must agree that we can have other reasons than direct observation, or demonstrations, for believing something to be true.
Maybe you should think about this principle a bit more.
The issue is the word “only” in that sentence. Obviously no amount of examples of intelligence producing codes* would constitute evidence that only intelligence can produce codes.
*(Not that anyone who thinks life originated naturally would dispute that designers can also produce codes.)
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Hmm, could you expand on this, it seems you are arguing, and I might be wrong, that any material construct or orientation which intelligence produces, like the configuration and orientation of matter comprising a car, would, with sufficient time, be produced purely by blind, unguided nature? That given enough time and opportunity, an explosion in a lumberyard will, eventually, produce a fully built house?
I’ve heard this line of reasoning before, and I wonder if this is your position here?
No. What I am saying is if energy flows can move matter around, it’s possible there is a pattern of energy flows that can move matter into those seemingly impossibly improbable-to-get configurations. Energy flows come in many different forms and patterns (besides explosions in junkyards, which are ironically incredibly rare), and there are still many we have yet to characterize or understand. They are extremely sensitive to local conditions.
Did you know that a heat flow in a microscopic rock pore system can collect and assemble the diluted components of a cell, each inactive because they are disassembled and distant from each other, so they become active and start to express genes?
Curious what these physical disequilibria can accomplish, isn’t it? Perhaps we don’t know everything there is to know about how “energy flows” can order matter.
I hereby claim that the above experiment demonstrated that an energy flow created functional organization.
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We’re discussing the origin of a functioning code — syntax, storage, and error correction. Apart from its scale, in what principled way is the genetic code different from any other coding system we know to exist, all of which are, as a matter of course, attributed to an Intelligent source, even if that source is unknown?
All intelligent sources known to exist are products of evolution.
Perhaps “known to exist” isn’t all you’re pretending it is.
Hmm…
@Thacker , when you are writing an draft using word processing software, when you make an error, does the code immediately throw away all of your work and have you start over? That’s what happens in living cells.
How often every day do you replace all of the components of your computer? If the answer is “almost never”, then your computer is nothing like a living cell. Living cells turn over their components constantly. (This consideration also applies to analogies between machines and living cells.)
Does the code that runs your computer demand that you rip out the power unit (NOT flip a switch) every time you shut the computer down? If not, then that code is nothing like what goes on in a cell.
How much of any code you know of is devoted to self-destruction? Arguably as much as half of the “code” in living things is devoted to self-destruction.
The fact of the matter is, this particular analogy is superficial and falls apart once one looks closely at what goes on inside of living cells.
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Just to make sure we’re talking about the same thing, the term “genetic code” refers specifically to the mapping of codons to amino acids as part of the translation process in cellular biology.
The primary difference is directly in the definition: the genetic code occurs within biological processes governed by biochemistry and is not a human invention, as I presume your other example of artificial codes will entail.