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Irreducible complication

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Re: Irreducible complication
Post by DDHv   » Sun Nov 12, 2017 11:15 pm

DDHv
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BJ fell, xrays, operation, weeks of therapy, and each visit chewed several hours from my day. I've not had time for luxuries such as this!

Most people who know statistics learned the frequentist version. This gives exact answers, but requires either a correct theory, or a large number of trials. Even so, it can only give the odds for classes, with no ability to speak to individual cases.

The less known Bayesian statistics does not give exact answers, but is usable for single cases. This is like a doctor who does not want to know the class figures for a given disease, but wants to know whether his patient has it. Many dislike Bayesian statistics because it uses estimates. An modifying estimate can be a frequentist answer, provided that form of statistics is applicable.

Note that since we only have evidence for one universe, the Bayesiam method applies.

To apply to the current question:
You start with prior estimates. For this, let us give priors of 20% probability to, alphabetically; Animist, creationist, mindist, naturalist, and to be complete, none of the above. The last allows those who say no meta-narrative (except their own) is possible a place in the list.

If changes are required to come from basic logic and experiment, this is a formalization of the scientific method.

To introduce one piece of evidence.

The assumption is 10^80 atomic particles in the known universe;
Make further assumptions of 10^18 seconds (about 30 billion years);
10^12 events per second for each particle;
yields a total possibility space of 10^110 events. Anything requiring more than this can be considered impossible.

In Darwin's day, he could describe the simple bacteria as slime. Today we can look at and even modify details. Example

McLaughlin, R. N. et al. The Spatial Architecture of Protein Function and Adaptation. Nature. Published online before print, October 7, 2012.

Later research:

Tirka, B. Why poison dart frogs don't poison themselves. PhysOrg September 5, 2017

and,

Wang, S.Y. and G.K. Want 2017 Single rat muscle Na+ channel mutation confers batrachotoxin auto resistance found in poison dart frog. Phyllobates teribilils. Proceedings of the national Academy of Sciences 114(30): 10491-10496.

Which came first, the poison or the immunity?


Researchers used experiments to estimate the ratio of randomly produced protein strings which can make stable folds to those which cannot. The smallest estimate I know is Sauer's work at 1 in 10^63. Doug Axe noted two problems with the work, one which would produce underestimates, one over estimates. His experimental work comes to about 1 in 10^74 for stable folds with worse odds if they are required to be functional.

Assume the actual odds are 1 in 10^55 power. Calculate the odds of getting two or more functional proteins. Apply this to modify each of the five priors. Don't forget that large valley space between the mountain peaks of stable fold ability. Never forget that a thing must exist before it can evolve.

This can be done for many other such things, such as the odds of two inter-functional proteins being in close enough proximity to work by chance plus time. The Bayesian method is a series of approximations to reality.

This can be applied to the quark >particle >atom >molecule >biomolecule >life hierarchy. Each level's properties depend on those of the next lower level. Most periodic table columns have similar results, with minor changes between rows. Without the properties of Oxygen, carbohydrates couldn't exist. Compare these properties to those of sulfur etd. Or just adjust the electromagnetic force constant > nuclear force constant ratio and see the results. AFAIKS the only way to have our functional universe without intelligent design is a multiuniverse with variant basics for each. This is philosophy, not science, since we don't observe any such universes.

It is far too easy to miss basics:

Also, and I once more have to repeat this because apparently it hasn't entered your skull yet: We have ample evidence that chance and time (as moderated by the mechanisms of evolution) can produce astonishing complexity; this article describes one such experiment (TL;DR: A researcher used a genetic algorithm to configure an FPGA over multiple generations until it reached a specified goal, in this case the ability to distinguish between two audio waveforms.


This experiment made the same error that Dawkin's modified alphabetical string thought experiment did: ignoring that specification of the end result and comparison tests are inputs of information, reducing the odds. To address Dawkins, there are many shapes which are not letters: there are many letter combinations which do not form words: there are many word combinations which do not form phrases; etc. The probabilities of a non-functional result are very much higher than getting a functional one, even just on the letter group level.

The elephant in the room is the exponential expansion of combinatorial inflation as the number of requirements for success increases. Those who smuggle functional information into their experiments while insisting on time and chance as the only answer insist there is no elephant. ID proponents don't think that trumpeting sound is some bugler practicing. They don't think those drafts in the room come from an open window. There are even atheists who accept ID.

If you want to say the last is illogical, I agree!

People tend to pick their philosophies for non-logical reasons - the question is whether they have enough faith in logic and experiment to use them to test their ideas. I know where my bias comes from: at age 15 I only went to church because of the family. A Hungarian lady was speaking Wednesday, and mom nagged me into going. I became aware that perfect judgement on me, from largest to smallest action, would condemn me. At the end, the offer was made: "Come forward, and after we have dismissed the service, we will show you from the Bible how to be forgiven." Later I realized this included the unspoken part - perfect forgiveness from the greatest to the smallest sin with God remaining totally honest. They showed me several places - the one that reached me was Isaiah 53:4>5. I went home rejoicing, and still do.

Eventually I realized that trusting God required my best effort at going by evidence - otherwise it would be the insult to God of living a lie. The right is reserved to test anything to see whether proposed evidence against God has any logical or experimental fallacies.

Example: Kurdish independence: The Kurdish people are still in their homeland, they have not left it for generations and then returned. I don't know of any non-Israelite people who have. The low probability is not forming the Israel nation, but remaining a people while exiled over generations.
Douglas Hvistendahl
Retired technical nerd

Dumb mistakes are very irritating.
Smart mistakes go on forever
Unless you test your assumptions!
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Re: Irreducible complication
Post by The E   » Mon Nov 13, 2017 6:26 am

The E
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DDHv wrote:This experiment made the same error that Dawkin's modified alphabetical string thought experiment did: ignoring that specification of the end result and comparison tests are inputs of information, reducing the odds. To address Dawkins, there are many shapes which are not letters: there are many letter combinations which do not form words: there are many word combinations which do not form phrases; etc. The probabilities of a non-functional result are very much higher than getting a functional one, even just on the letter group level.


Do you understand what evolutionary pressures are?

I'm seriously wondering here: Do you realize that evolution isn't just random mutation, but random mutation moderated by the environment? That you cannot remove one factor and still call it evolution?

Specifying a desired goal in experiments like this is a necessary prerequisite for running them, just like a natural environment is a necessary prerequisite for evolution in the wild.

The elephant in the room is the exponential expansion of combinatorial inflation as the number of requirements for success increases. Those who smuggle functional information into their experiments while insisting on time and chance as the only answer insist there is no elephant. ID proponents don't think that trumpeting sound is some bugler practicing. They don't think those drafts in the room come from an open window. There are even atheists who accept ID.


You really do not understand anything I say, do you.

If you want to say the last is illogical, I agree!


There's one source of illogical reasoning here, and it's you.

People tend to pick their philosophies for non-logical reasons - the question is whether they have enough faith in logic and experiment to use them to test their ideas. I know where my bias comes from: at age 15 I only went to church because of the family. A Hungarian lady was speaking Wednesday, and mom nagged me into going. I became aware that perfect judgement on me, from largest to smallest action, would condemn me. At the end, the offer was made: "Come forward, and after we have dismissed the service, we will show you from the Bible how to be forgiven." Later I realized this included the unspoken part - perfect forgiveness from the greatest to the smallest sin with God remaining totally honest. They showed me several places - the one that reached me was Isaiah 53:4>5. I went home rejoicing, and still do.


...and? That must automatically mean that every single thing in your holy book must be truth, the whole truth and nothing but the truth?

I don't think so.


Eventually I realized that trusting God required my best effort at going by evidence - otherwise it would be the insult to God of living a lie. The right is reserved to test anything to see whether proposed evidence against God has any logical or experimental fallacies.


I am glad you agree that creationism is bullshit.

Example: Kurdish independence: The Kurdish people are still in their homeland, they have not left it for generations and then returned. I don't know of any non-Israelite people who have. The low probability is not forming the Israel nation, but remaining a people while exiled over generations.


Non sequiturs are not the effective rhetorical tool you wish them to be.
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Re: Irreducible complication
Post by DDHv   » Tue Dec 12, 2017 7:58 am

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The E wrote:..and? That must automatically mean that every single thing in your holy book must be truth, the whole truth and nothing but the truth?

I don't think so.


You might try walking through the eastern gate of Jerusalem. Prophecy, Ezekiel 44:1-3 and (still future) 46:1-8. Time of prophecy approx. 571-560 BC. Suleiman the Magnificent of the Ottoman Empire rebuilt the walls of Jerusalem 1537-1541 AD. Two minor gates were also blocked and have been reopened. The eastern one is still blocked and is the only major one which was shut. There have been several times in between when said walls were destroyed and rebuilt. It would be interesting to get more details on that.


Please explain how to have evolution before you have reproduction. The odds against replication even on the chemical level are so high that the total number of atomic level events in a tens of billions year universe still wouldn't provide enough events for replication to start being probable.

Can a race be run if it isn't started?
Douglas Hvistendahl
Retired technical nerd

Dumb mistakes are very irritating.
Smart mistakes go on forever
Unless you test your assumptions!
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Re: Irreducible complication
Post by The E   » Tue Dec 12, 2017 8:22 am

The E
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DDHv wrote:Please explain how to have evolution before you have reproduction. The odds against replication even on the chemical level are so high that the total number of atomic level events in a tens of billions year universe still wouldn't provide enough events for replication to start being probable.

Can a race be run if it isn't started?


We've been here before. These are points you brought up pages and ages ago, and just as they were back then, they are now little more than a confirmation that you are unwilling to read the relevant science outside of the creationist bubble you are in.

It's astonishing, actually. Do you have any idea how disrespectful it is for you to not do your homework, but rather expect me or others to do it for you?
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Re: Irreducible complication
Post by gcomeau   » Mon Dec 18, 2017 3:06 pm

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DDHv wrote:
The E wrote:..and? That must automatically mean that every single thing in your holy book must be truth, the whole truth and nothing but the truth?

I don't think so.


You might try walking through the eastern gate of Jerusalem.


Because that will prove exactly nothing?

Please explain how to have evolution before you have reproduction. The odds against replication even on the chemical level are so high that the total number of atomic level events in a tens of billions year universe still wouldn't provide enough events for replication to start being probable.

Can a race be run if it isn't started?


Getting old, not up to date on the current state of the research, but still a good explanation of the concepts involved and the utter BS of your statistical argument.

If, of course, you bother to actually read it.

http://www.talkorigins.org/faqs/abioprob/abioprob.html
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Re: Irreducible complication
Post by DDHv   » Sat Feb 10, 2018 8:13 am

DDHv
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gcomeau wrote:
If, of course, you bother to actually read it.

http://www.talkorigins.org/faqs/abioprob/abioprob.html


Thank you for the reference, it is one I've not seen before. I also sampled the bibliographies.

You might want to look up Hubert P. Yockey's work. I especially like his definition of the key difference between life and non-life. FWIR this evolutionist was an early pioneer in using information theory in biology questions. I've not yet read "Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life 2005 Cambridge University Press," but it is now on my 'to read' list.

With BJ home and active, there is again time for hobbies. Re your reference:

His discussion of a "primordial protoplasmic globule" assumes that enclosure is the only needed function. His later discussion of macromolecular assembly shows the error. He is correct in stating the sequence argument is incomplete, but ignores the chirality barrier, the non-peptide link barrier, and the chemical poisoning barrier, so it is also incomplete. Chirality doubles the number of reactions, non-peptide linking approximately doubles it again. Just with these first two, the calculated number for probability is changed by 4^32. I won't even guess how many chemicals would poison the reaction. I suspect the difficulty of making a decent estimate here is why this isn't mentioned often. Wikipedia states there are hundreds of amino acids alone, with the only the standard 20 used in proteins. Can the pure solution he posits for his calculations exist by chance? Oceans, or even ponds full of just the standard 20 AA?

He should not state "so that a fair number of efficient RNA ligases (about 1 x 10^34) could be produced in a year," without adding the phrase 'unless interfering chemicals cause the reaction to go wrong.'

The theory he favors has simple chemicals, polymers, and replicating polymers (in a pure solution) observed, and the remainder until bacteria hypothetical at the time he wrote. Darwin suggested that later fossil discoveries would close the gaps between phyla. We get a punctuated equilibrium theory. Should we expect a "hopeful chemical" theory later?

An irreducible complication: If the Ur cell membrane does not allow needed reactants in, the reactions starve. If allows poison chemical entry, the reactions are destroyed. If the reactions do not replicate a working membrane can there be replication? Experimental swapping of a donor nucleus from a different kind of eukaryote into a host embryo show that the host continues to grow along its epigenetic pattern until the wrong nucleus doesn't provide all of the needed chemicals.

Cancer chemotherapy depends on cancer cells absorbing more poisons than normal cells. The cesium chloride protocol is effective, but requires supplements since absorption of CeCl increases cancer's absorption of other chemicals (which normal cells need). BTW, immunotherapies look very promising. FWIR, the PD-1 versions, targeting about 30% of cancer types, are so effective that a warning was issued stating that sometimes the tumor would disappear between doctor visits! May the researchers do very very well!!

To be blunt, the search space is much larger than he proposes unless a cell membrane much more sophisticated than he allows for is able to do selective filtering. There is also the problem of the rarity of stable folds. Someone should follow up on the research here: an evolutionist should be interested in the question of whether smaller proteins have a higher probability of having stable folds - I've not seen any work on this question yet.

In thermodynamics, I was taught that the path between two states does not determine the difference between them. I also learned the 2nd law - a version of Murphy's law. The variation I like best is "Anything that can go wrong will go wrong, unless someone makes it their business to prevent it." The latter phrase is the sticking point for ID opponents. They remind me of the idolators who would use materials obeying mechanical laws and expect non-mechanical results.

The existence of varied basic assumptions has the advantage of producing a larger search space for useful experiments in science. Humans willingly ignore observations which invalidate our own assumptions unless we make it our business to sample the work of those who don't agree.

BTW, a variation on the chicken and egg conundrum: Which came first, the poison of poison dart frogs, or their own immunity to it? I'd like to find where someone addressed the question of why these frogs don't dominate their surroundings if they are truly predator free ;)
Douglas Hvistendahl
Retired technical nerd

Dumb mistakes are very irritating.
Smart mistakes go on forever
Unless you test your assumptions!
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Re: Irreducible complication
Post by Daryl   » Sun Feb 11, 2018 7:05 am

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As to "BTW, a variation on the chicken and egg conundrum: Which came first, the poison of poison dart frogs, or their own immunity to it?", the simple answer is that they evolved together over much time, as in all similar cases. If not there would be no poisonous creatures.
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Re: Irreducible complication
Post by dscott8   » Mon Feb 12, 2018 12:28 pm

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Re: Irreducible complication
Post by The E   » Tue Feb 13, 2018 5:04 am

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DDHv wrote:In thermodynamics, I was taught that the path between two states does not determine the difference between them. I also learned the 2nd law - a version of Murphy's law. The variation I like best is "Anything that can go wrong will go wrong, unless someone makes it their business to prevent it." The latter phrase is the sticking point for ID opponents. They remind me of the idolators who would use materials obeying mechanical laws and expect non-mechanical results.


This is your scheduled reminder that, for all the talking you've been doing, all the reading you've claimed to have done, and all the talking and researching ID proponents have done over the years, none of them have been able to formulate a testable hypothesis about the mechanisms of creation that invalidates the theory of evolution.
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