Do you have an example of someone who has reproduced Axe’s experiment?
Then why do you keep pointing to highly conserved sequences as examples of functional information?
Why hasn’t Axe repeated his experiment with a number of other samples?
I’m not sure where to go with this. The initial problem was the Mount Rushmore-fifth face problem. I sketched out a possible solution to the problem, but there seems to be so much confusion about function, functional information (FI), ID, and whether cancer can produce FI, to name a few, that I don’t think anyone would follow me if I now do a more detailed examination with actual estimated values for the variables of the solution I proposed.
@T_Aquaticus took what I view to be the first correct step toward solving the original problem … proposing that we need some sort of mathematical definition and a way to measure the p-value, etc. I then provided a mathematical definition and sketched out how I would approach the problem. I could do a more detailed pass, defining variables, getting some approximate normalized numbers, the way we normally do things in science problems, but I think some confusion needs to be addressed.
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Some are under the impression that I think that new functions are impossibly improbable for natural processes to produce. That is complete rubbish and I’m mystified as to why people invent beliefs and then assign them to me. The function of an F-22 aircraft might be difficult for natural processes to achieve, but the function of producing ripples on a puddle by a dripping icicle, is easy to achieve. There are countless functions that require little or no new FI.
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Everyone is free to make up whatever mathematical definition for functional information that they like, so long as it gives meaningful results. My own definition for FSC (which in the paper I state is equivalent to FI) is published in my paper I referenced earlier. The FI required for an effect is the difference in Shannon information (∆H) between the ground/initial state of the physical system and the functional state. Simply put, it is FI = ∆H. This method can measure both FI gained (+ve) and FI lost (-ve). It also gives meaningful results when applied to the sub-molecular structure of ubiquitin.
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Since the K-L divergence always gives a +ve answer, it is not a good method to measure FI when we test it with a case where FI is lost and should yield a -ve answer. We need a measure that handles all cases, both gain and loss of FI. My method does that.
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I’m puzzled why some posters describe FI = ∆H as “arbitrary”. We all agree that H = Shannon information, and we all agree that ∆H is the change in information between two states. If the initial state represents the ground state, and the other is the functional state, then we have the amount of information required to achieve that function. This is neither arbitrary, nor rocket science. Furthermore, high FI correlates with highly constrained sub-molecular areas and binding sites, exactly as we would predict, so it is not only non-arbitrary, but it gives useful results.
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Neither Shannon information, nor mutual information, nor K-L divergence will, by itself, give us FI. It must be meaningfully associated with a defined function, or set of functions. One can find a huge value for mutual information and have zero FI. As Szostak pointed out in his nature paper, classical information should not be confused with functional information.
So there are two ways to go from here: 1) do a methodical, more detailed pass on the rock face problem originally proposed to demonstrate that my method gives meaningful results in the field or, 2) pause the problem and read Josh’s cancer paper to see why his approach to FI gives highly questionable results when it comes to cancer. Since Josh is the original poster of the problem, just let me know which option you’d prefer to see me address and I’ll proceed accordingly. I’m leaving in the morning to do some ice fishing on Lake Manitou for the weekend, so I’ll pick this up on Monday.
All good theories start out as intuitions, but not all intuitions make good theories. We can’t base scientific conclusions on our intuition of how nature works. We need a bit more than that.
I would be interested to see how you would apply this to catalytic antibodies.
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For this thread we should focus here. We went off topic (sorry) and the FI questions arose mainly in response to your answer on the face.
It seems your answer there is really ad hoc. The fifth face just doesn’t look designed to you, nor does mount Everest. You have some criteria for why, they these criteria seem invented for this idiosyncratic case, and are therefore difficult to take seriously. I still have a have a hard time getting my head around this. Mount Everest screams “God’s creation” to me but you say it doesn’t look designed. The fifth face of Rushmore is far more impressive to me than the four. Biology looks far more like Everest and the fifth face than it looks like the four faces. It screams “Gods creation” to me but look nothing like piddly human designs. I just can’t understand yet why you would abandon the awe and wonder of Everest to hone in on the “design” of Rushmore. If this is what “design” is reduced to, perhaps God did not design us after all, perhaps he instead created us.
I honestly don’t think it would. What would that tell us? So he calculates some value of FI for a class of antibodies, what do we now know that we didn’t before? What can we use that information for? Absolutely nothing.
It’s all smoke and mirrors done to “dress up” what amounts to a question-begging claim against evolution in the technical jargon of information theory.
How so? And is Mount Everest unusual in this way or does every object in the world scream the same thing?
Ok. I’ll pick up this up on Monday, and I think I can provide objective answers to your questions.
I’ll take a look at it. I may have a question or two for you, for clarification.
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Back to the five faces problem for a more detailed analysis …
A. We need a baseline (or a “ground state”) from which to work. The most basic ground state is the laws of physics and the initial conditions of the universe. The result is what we can call “natural processes”. Are the laws of physics and the initial conditions of the universe designed? Josh believes they are, and I would concur. We need not all agree on this, however, for the purpose of this problem.
B. Within the scope of natural processes, a lot can happen, but they still seem to be inadequate to produce a smart phone, or an MRI machine. These require something in addition to natural processes. They need a higher level of design and one thing that is required for this higher-level design is intelligence. Thus, we have a definition for intelligent design …
Intelligent design: an effect that requires intelligence to produce.
C. Examples of intelligent design include the Canon EOS R, a flight simulator, Handle’s Messiah, Michelangelo’s David , and John Milton’s Paradise Lost . In every case, we can describe those effects in terms of information. This provides us with a way to test for intelligent design, in terms of meaningful or functional information. The term “functional” is used for reasons explained by Szostak in his short Nature article cited earlier. My approach is to estimate the difference in Shannon information between the functional and non-functional (or “ground”) state. This will give us the amount of information required to produce the function as follows …
FI = ∆H = -log2 (Wf/Wt)
This is a simplified version of the more general case, which does not assume uniform probability, but this simplified version will do for the five faces problem.
D. For each of the three problems presented by Josh, we need to get some idea of what Wf/Wt is. It would be helpful to define at least one or two attributes of the three test cases that we can apply to all three to estimate the probability Wf/Wt of each of them, and then estimate the amount of intelligent design required for each.
E. Let me suggest just two:
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symmetry: Does the effect show any signs of symmetry? How much symmetry does it show? If the effect displays symmetry, we can divide the effect into symmetric sections reminiscent of finite element analysis to quantify the symmetry of some given degree, and from that, estimate the probability of obtaining that degree of symmetry by natural processes.
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Sharp relief vs relative smoothness: Sharply defined relief is common, but the processes that produce smoothness also wear down sharply defined relief. Therefore, if we observe smoothness that is out of place relative to the surrounding area, coupled with sharply defined relief, we have something objective with which to quantify an anomaly.
I’ll stop here for the moment to see if we can all come to some sort of agreement as to how we can objectively evaluate the three possible anomalies suggested by Josh. Imagine you are part of a field team sent out to evaluate and quantify an anomaly and you must come up with some objective criteria with which to do it. I’m open to other criteria, so please feel free to contribute to the analysis of this problem as a team, and we will then proceed from there.
Can you explain what you mean by the term “natural”, and what about their origin is “unnatural”?
Sometimes. Not always. A mountain stream cutting through granite or marble produces both high smoothness and sharp relief. Rather like Henry Moore sculptures, in fact.
But I think your biggest problem is in B and C, when you reason from a smart phone to the general case; if natural processes can’t produce a smart phone, then they can’t produce anything with lots of “meaningful or functional information”. That’s just not a valid inference.
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It’s not obvious to me that “natural processes”(whatever that is supposed to mean) didn’t actually produce smartphones.
I really cannot believe that all this smart sounding scientific bantering over feelings…to one person, mt everest feels like creation but does not feel like design. And they make their fancy sounding scientific case to justify their feeling. The other has feelings that hones in on design of rushmore that accordingly is seemingly accused of reducing the splendor of everest to for God’s and uses a lot of fancy language to make his case.
I can think of no better Biblical text than Job where there was so much philosophical bantering over feelings from both sides of the equation about what caused Job’s condition. How did that really savy sounding discussion/argument end? God showed up and told everyone to shut up. He asks all parties “where you there when i created…designed… etc” He ultimately pointed to Job as being more right, but still made it quite clear that Job is still a frail miserable little creature next to His glory and Being.
He has to be watching this discussion and the detail of scientific argumentation and laughing His head off at how we think we are so smart. We think we know things because we feel certain ways or see how cancer causes fi or how the science plays out.
Did God create and design Everest? Yes. He designed the geological system on earth to be able to form mountains. And He can design and create a mountain directly. And we have to remember that perhaps the mountain formed as a result of the fall where the earth was subjected to futility and caused geological patterns to change resulting in forms like Everest. Who knows. Mountains are one type of creation that God is sovereign over. And humankind is ANOTHER kind of creation and design. God designed human kind in a different way than the mountains were designed and created. And we can know this because man was designed and created in Gods image and mountains were not. Do we need a scientific computation to determine that?
I think this scientific back and forth is going to be a waste of time. Both sides will give their science to back their feelings and wont budge. And if God showed up, He’d tell everyone to shut up. He’d probably continue with admonishing all parties the foolhearty nature of trying to use science to prove items already clearly said by Him in His word. And like in the book of Job, He would probably chose the side closest in proximity to what He said through His prophets which is the truth of all truths to pray for the other side.
This is unbelieveable. AIG and ICR is looking better and better when i see this waste of energy.
This long waste of time from which many books will be writtten and profitted from seems to point to the better Book being the wisest path and books that promote that are worthy of our attention.
Yes, humans are part of nature.
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Only if you like being lied to and told what you want to hear.
Reality is a scary place for you, eh Greg? 
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“You can safely assume you’ve created God in your own image when it turns out that God hates all the same people you do.” - Anne Lamott
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Reference to Job 38:
"Then the Lord answered Job out of the whirlwind and said:
2 “Who is this that darkens counsel by words without knowledge?
3 Dress for action like a man;
I will question you, and you make it known to me.
4 “Where were you when I laid the foundation of the earth?
Tell me, if you have understanding.
5 Who determined its measurements—surely you know!
Jobs appropriate response to God in Job ch 40:
3 Then Job answered the Lord and said:
4 “Behold, I am of small account; what shall I answer you?
I lay my hand on my mouth.
5 I have spoken once, and I will not answer;
twice, but I will proceed no further.”
And God hates sin but loves everyone! John 3:16. But He is not a needy God who bends to conform to us unless He sees fitting in His love for us. He loves us enough to offer reproof.
By “natural”, I mean processes that are determined by the laws of physics when applied to space, time, matter, and energy. Within this framework, we observe a special category of effects … those that are associated with intelligence, like a smartphone, for example. Now it is true that all the molecules required for a smartphone could spontaneously come together to form one, but the probability of that happening is infinitesimally small in comparison to the probability of intelligent agents building a smartphone. So the more rational position to take is that intelligence is required to build a working smartphone, at least if one wishes to get it before heat death sets in on the universe.
As I suppose you realize, a Henry Moore sculpture is an example of intelligent design. In my own observations, which are substantial since I’ve spent a great deal of time in the wilderness over the past 30 years, erosion smooths out the sharp edges of larger scale features. Of course, you are welcome to suggest some other variable we can use instead or in addition.
As I mentioned above, natural processes can, in theory, produce the next generation of smartphone, but we can get them a lot sooner if we apply intelligence into the mix.
I assume no one here actually can’t tell the difference between a high-tech, state-of-the art device, and a section of wilderness swamp. That being the case, what objective method would you use to distinguish between all the stuff we build today, and a pile of rubble at the base a cliff? For those of you who are scientists, you need to come up with a method to do this, preferably a mathematical equation as T_aquaticus suggested. The method I suggest is functional information; it is one of the “fingerprints” of intelligence. It isn’t the only fingerprint, but it is one of them. This does not mean that natural processes cannot accidentally produce a fingerprint–just that is is not very probable.
What does probability have to do with functional information? Well, the primary variable in calculating functional information is, for our purposes, Wf/Wt, which is a probability. The amount of informational bits required is inversely proportional to its probability … that is the math behind equations for information. This does not mean that nature cannot do it without the aid of intelligence, just that it becomes extremely improbable without intelligence.