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Thursday, August 04, 2016

This anti-science creationist could be Vice-President of the United States of America

Thanks to PZ Myers for digging up this speech by Mike Pence in the House of Representatives [Mike Pence, creationist]. I think Pence is trying to make America great again by returning the country to the stone age.




275 comments :

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Diogenes said...
This comment has been removed by the author.
Anonymous said...

Cruglers, that didn't help me figure out what you meant. When you wrote, "Why? Because if there was such evidenced, intelligence, though very limited, should have already surpassed the random processes that apparently brought life into existence, should they?" what were you trying to say?

Was SRM correct when he wrote, "He is essentially trying to say that our highly organized intelligence should already understand the origin of life if it arose from dumb random chemistry."?

Unknown said...

Diogenes wrote:

" So it's off to a new 'chicken and egg': "the enzyme by itself even fully formed, would have no use, unless the DNA double helix molecules were already existing as well".

Well, you just assumed that and you assumed wrong. As I already pointed out, at least one of those enzymes, DNA polymerase, has another function: replicating viroid RNA. "

So ? How does that refute what i wrote ?

Fair Witness said...

Cruglers: If I was an omnipotent being, and I had designed something like humans, with all their imperfections and frailties, I might hang my head in shame and be glad someone else was taking credit for it. If I was REALLY omnipotent, and had my shit together, I would create another supreme being to be my companion, not puny humans.

Jmac said...

You are not even a moron Oberski, so I'm not going to waste time on your incoherent delusions. Educate yourself about "omnipotent, omniscient friend" and where this came from. Then we might talk.

Jmac said...

FW See my comment to Oberski.

Jmac said...

I think that to have a real conversation whether origins of life can be considered science vs science fiction there has to ONE reliable definition of life. Once that is established, some might speculate whether the first form of life could have formed by random processes.

Unfortunately, there is no consensus among scientists as to what life really is and how to define it. Consequently, to make claims that there is evidence that life could have come about on its own (whatever the claims are and circumferences surroundings the claims including observation-meaning: there is life and nobody makes the claim to be the originator, therefore it must have come about by accident) is just as preposterous as a claim that a battery operated robot self-assembled and then self-generated power to operate itself without having any source of "direction" to self-assemble and any source of power to accomplish those tasks.

BTW: Diogenes; Don't make comments about your theory of the Sun being the source of power for the origins of life because I will ignore your comments. Unless you can prove scientifically that the power generated by the Sun can have the some application as the electric power used in tools to build/create thingswithout direction or an intelligent tool operator.

To build a shack, one needs to power his tools to accomplish his task.Sure. But tools like drills, nail-guns, saws and so on will not accomplish the task of building the shack without intelligent direction to apply the tools to make the precise tasks even if they have trillions of years to do so.

Jmac said...

Diogenes

Does anybody have a copy of the Axe 2004 paper that they can email me? It's behind a pay wall, but I want to find out where his math went wrong.

You are such a great scientist and you don't have access to pay-walled articles??? The housekeeper that takes care of my office has access to that because he works for this institution. I'm going to ask him to email you the few dollar article, so that you can feel good.

Now, let's get to the meat an potatoes of your claims about D Axe and A. Gauger experimental evidence with your excuses that they used wrong proteins... this... and that.

Now, let's see links to the experiments you have preformed that prove them wrong. Let's see experimental evidence that proteins can evolve new functions in timely matter for evolution to be a valid theory. If poor, disadvantaged creationists with almost no budget could provide evidence that evolution is wrong, I'm sure that yours and tens of thousands of scientist who enjoy the benefits of tax payers grants can resolve this issue in no time.





Diogenes said...

Cruglers, are you Witton or some sock puppet for the creationist idiots who got banned from here? Because the phrase "You are such a great scientist and you don't have access to pay-walled articles???" sounds exactly what previous creo sock puppets have said. Some creos get obsessed with me personally and go on "Oh, Diogenes is a great scientist" when in fact, I've never called myself a scientist and, being anonymous, I've never boasted about any credentials and no one here even knows my fields of specialization, if I had any. But certain creos fixate on it.

"Let's see links to the experiments you have preformed that prove them wrong." Uh, I don't have to do any experiments, I linked to the Szostak paper above which proved Axe and Gauger wrong. No need to do the same experiments twice. I can, however, pick apart Axe's math errors without doing experiments. You don't need to do experiments to prove 2+3 is not = 10^77.

"If poor, disadvantaged creationists with almost no budget..." Wha..? Creationists are poor? Ken Ham is swimming in taxpayer dough.

The budget for the Discovery Institute is $5-6 million per year. They choose to send ONLY about $200K -$300K or so to the Biologic Institute (Doug Axe and Ann Gauger), their alleged "experimental" arm. If Axe and Gauger are "poor", well, remember that the rest of the DI's $5-6 million budget goes to lobbying politicians, a bevy of lawyers, Stephen Meyer's bloated salary, and airplane tickets for Lathey Flufkin.

"yours and tens of thousands of scientist who enjoy the benefits of tax payers grants"

Uh, creationism is funded by taxpayer money. In Louisiana and other states, "student vouchers" are used to pay creationist schools.

Ken Ham just built a $100 million dollar building that he calls a "boat" but which can never float, and that money mostly came from the taxpayers. Ham didn't do science experiments with that $100 million from taxpayers, he just built a building from Tyvek and laminate and steel joints, and called it a historic "wooden" boat, and put a couple dozen stuffed animals in it. Stuffed animals... very entertaining, I'm sure, for the four or five victims of churchly child abuse who are drug there every day.

Diogenes said...

This statement is ridiculous: "Homology can well be explained through common design. Thats common practice." No, "common design" is creationism, and creationism does not "explain" homology. A rational explanation is not the same as a story about an unusual cause. An unevidenced story about a bizarre cause is at best a hypothesis, at worst a fairy tale, but merely alleging an unusual cause is not a rational explanation. Creationists redefine the meaning of the word "explain" where their pet hypothesis is concerned.

A rational explanation can only be of two types, 1. a deduction from well-known principles previously inferred, or 2. an extraordinary claim supported by extraordinary evidence, typically via the scientific method. "Common design" is neither 1 nor 2.

As for 2, common design cannot be shown through the scientific method because it is non-falsifiable. What evidence could NOT be produced by a "common designer" (God) that is unlimited, omnipotent, and whose purposes and intents are unknown? If the common design hypothesis can accommodate all evidence, then it predicts nothing and thus cannot be falsified.

As for 1, common design cannot be deduced from homology because homology requires a phylogenetic tree converging to a unique nested hierarchy, and human-created artifacts can never be classified into a phylogenetic tree converging to a unique nested hierarchy. E.g., consider human-"designed" organisms like Pokemon, or the dragons in How to Train Your Dragon. They don't converge to unique nested hierarchy. By contrast, human languages do form a "tree" structure and their traits are not produced by a single Common Designer. So homology would NEVER lead to a deduction of common descent.

Without deduction or the scientific method, you're left just redefining the word "explanation" to mean a fairy tale of causation. Alleging causation is not enough. That is not an explanation in the scientific sense, it's only explanation in the fairy tale narrative sense.

Diogenes said...

Grasso: "The many similarities that exist among members of the animal kingdom can well be the result of the fact that a single designer created the basic kinds of living 'systems', then specially modified each type of life to enable it to survive in its unique environmental niche."

Again, non-falsifiable. An unlimited "designer" whose purposes are unknown could do the above, or do the opposite.

But let us try making predictions about organisms. Which of the following species would you predict to have:

A. lungs, B. wrists or ankles, and C. hair.

In:

(Filter feeders)
1. Blue whale
2. Whale shark.

(Fusiform Predators)
3. Dolphin
4. Tuna
5. Ichthyosaur

(Serpentine Predators)
6. Moray eel
7. The sea snakes Pachyrhachis and Eupodophis

(Top predators)
8. Orca
9. Great white shark.
10. Liopleurodon
11. Tylosaurus

(Seagrass eating herbivores)
12. Manatee
13. Marine iguana.
14. Leatherjacket
15. Garfish

In each group, e.g. "filter feeders" the species all DIFFER in their answers to questions A, B, and C above, but they all have the same lifestyle and ecological niche. That is, in each group with the same ecological niche, they differ in the presence or absence of wrists/ankles, hair, or lungs. What could explain the nonrandom pattern?

The pattern of anatomical similarities and differences can't be explained by alleged functional constraints, nor by omnipotent designers that are unlimited and yet at the same time totally limited by functional constraints. You CANNOT answer questions A, B, and C for all 15 species above merely by hypothesizing they were made by a "common designer." A common designer could have made any pattern of answers for questions A, B and C.

By contrast, with evolutionary theory and the hypothesis of common descent with gradual variation, you CAN easily and correctly predict the answers to questions A, B and C for all 15 species above.

Evolutionary theory emits specific predictions. "Common designer" does not predict, it accommodates all possibilities and patterns, it cannot exclude anything and thus cannot be falsified.

Diogenes said...

And Grasso says: "Examples which seem to fit evolutionary assumptions are cited, while the examples that do not fit are ignored"

Of course this is false. Scientists pay a lot of attention to apparent violations of the general rule and try to figure out why they happened.

The specific case that Grasso cites in TIC110 which he alleges has no homologs. But scientists clearly did not ignore this:

"Revaluating the evolution of the Toc and Tic protein translocons." Gross J1, Bhattacharya D. Trends Plant Sci. 2009 Jan;14(1):13-20. doi: 10.1016/j.tplants.2008.10.003.

Abstract: The origin of the plastid from a cyanobacterial endosymbiont necessitated the establishment of specialized molecular machines (translocons) to facilitate the import of nuclear-encoded proteins into the organelle. To improve our understanding of the evolution of the translocons at the outer and inner envelope membrane of chloroplasts (Toc and Tic, respectively), we critically reassess the prevalent notion that their subunits have a function exclusive to protein import. We propose that many translocon components are multifunctional, conserving ancestral pre-endosymbiotic properties that predate their recruitment into the primitive translocon (putatively composed of subunits Toc34, Toc75 and Tic110 and associated chaperones). Multifunctionality seems to be a hallmark of the Tic complex, in which protein import is integrated with a broad array of plastid processes.

Clearly these scientists did not ignore the problem. There are other papers.

This kind of accusation of concealment is common with creationists, as muggle audiences won't know any better and the accusation of concealment makes the muggles more suspicious of experts. But it is not "concealment" just because non-experts do not know what experts in the field are talking about.

How else would creationists like Grasso know about these apparent violations? Only because scientists pay attention to them.

The whole truth said...

Otangelo said: "Thus, it is clear, life could not have formed in the ocean."

Where, when, and how did life 'form', and what positive evidence can you provide that supports your claims?

Unknown said...

5. Is the answer God did it? Do I get a prize? I would love to take a degree in biochemistry at a creationist university. The answer to every question is, "God done that", and you get an A+ everytime!

Larry Moran said...

Be careful. Some of the correct answers won't be "God did it." For some questions the correct answer will be "evolution is impossible."

judmarc said...

Be careful. Some of the correct answers won't be "God did it." For some questions the correct answer will be "evolution is impossible."

This points out the logical contradiction at the heart of ID. The primary argument is "Evolution is impossible, therefore a Creator must have done it." But for the omnipotent, omniscient God of the Bible who is everyone's favorite candidate for Creator, *nothing* is impossible. Thus the premise, "evolution is impossible," is demonstrated to be false by the supposed conclusion.

Bill Cole said...

Diogenes
"
This means that the total number of invariant residues should be approximately constant as the sequence gets longer, assuming the function does not change and there are not multiple functions or functional sites. Thus the fraction of residues tolerant to mutation should go up as L increases. If we assume the functional site has a fixed size S, and all its residues are invariant, the numerator would be more like 20^(L-S), and the fraction would be like:"

I agree with your logic here. This is why I did not agree with Lutesuite that you could simply scale the numerator with the denominator because proteins have different substrates and some have multiple function. Also as you mentioned some are more mutationally sensitive. I also think non enzyme proteins need to be examined. I am interested in your critique of the Axe paper.

Diogenes said...

It's not relevant to RNA. No one thinks life started with singl stranded DNA.

Jmac said...

Diogenes,

Give me the link to the pay-walled article by D. Axe you can't get while I'm in the office. I'm leaving in 30 min.

Jmac said...

John Taylor,

5. Is the answer God did it? Do I get a prize? I would love to take a degree in biochemistry at a creationist university. The answer to every question is, "God done that", and you get an A+ everytime!

What exactly is your answer/question based on? Where did I say or insinuated that "God did it"?

Diogenes said...

Thank you for offering Cruglers, but lutesuite has sent it to me already.

Jmac said...

John Tayor,
If random processes did't do it and gods didn't do it either there maybe the third way. Maybe humans did it and then they tricked us all to believe the other 2 concepts. What do you think of that option?

Faizal Ali said...

Bill Cole, your initial claim was that the the number of functional sequences stays constant, or nearly so, so that as the number of possible sequences increases, the ratio of functional to non-functional sequences approaches zero. Are you now saying this is incorrect?

You also did not understand Diogenes' argument, but I'll let him correct you.

Bill Cole said...

lutesuite
Bill Cole, your initial claim was that the the number of functional sequences stays constant, or nearly so, so that as the number of possible sequences increases, the ratio of functional to non-functional sequences approaches zero. Are you now saying this is incorrect?"

This was not my claim. My claim was that it was unlikely to scale with only sequence length. It should be correlated with function type, size of substrate and how many functions formed and how may different molecules a protein binds to. So the size of the ratio will decrease with the complexity of the protein.

I do not think this is inconsistent with Diogenes argument except his claim that it will scale if function stays the same because he is ignoring the additional complexity of proper folding of proteins as AA count gets larger. Chaperones exist for a reason.

Faizal Ali said...

So it seems that you are only concerned with the odds of a particular specific protein evolving, rather than with likelihood functional proteins of any sort arising thru evolution. If so, that is the error that has repeatedly been pointed out to you, and which you deny making.

Bill Cole said...

lutesuite
"So it seems that you are only concerned with the odds of a particular specific protein evolving, rather than with likelihood functional proteins of any sort arising thru evolution. If so, that is the error that has repeatedly been pointed out to you, and which you deny making."

This is a disagreement we have. I don't think your model is an accurate representation on how biology works, especially with proteins that interact with each other. You can't just build proteins that bind with anything and expect to build a living organism.

I will be out of pocket the rest of the day. I am interested if you really think you can back up your claim that evolving proteins with generic binding activity will lead to a living organism. You may want to start with Dr Ventner's 473 gene bacteria as a starting point.

Faizal Ali said...

@ Bill Cole.

As is so often the case with you, your response seems to have nothing to do with what I wrote. Maybe you can explain what you mean when you say, "You can't just build proteins that bind with anything and expect to build a living organism." I suspect this is just more sloppy writing on your part, but taken at face value that is not something that I, nor any competent biologist, has claimed.

If, OTOH, you are talking about enzymes evolving from more "promiscuous" ancestors, then that has been demonstrated empirically:

http://sandwalk.blogspot.ca/2012/07/the-evolution-of-enzymes-from.html

Bill Cole said...

lutesuite
"So it seems that you are only concerned with the odds of a particular specific protein evolving, rather than with likelihood functional proteins of any sort arising thru evolution"

Can you explain what you mean by the above. I guess I don't understand your argument.

Faizal Ali said...

Here's what your wrote:

So the size of the ratio will decrease with the complexity of the protein.

You refer to the protein. So, if we're talking about the odds of one specific protein evolving, you are correct: The larger the protein, the less likely it is to evolve. Just as you are less likely to win a lottery with 1 million possible numbers than one with 1000. But that argument is meaningless. What you need to calculate is how many possible different structures of proteins can perform some function, any function. This would even include the same function as the protein you are talking about, but with a different sequence of amino acids. That is one of Diogenes' points that you failed to grasp.

Bill Cole said...

lutesuite
" What you need to calculate is how many possible different structures of proteins can perform some function, any function. This would even include the same function as the protein you are talking about, but with a different sequence of amino acids. "

" What you need to calculate is how many possible different structures of proteins can perform some function, any function."

If I do this calculation what have I learned? What does any function mean? Can you give an example?

Faizal Ali said...

I don't really know one would perform that calculation, or if it is even possible to do so. But since that number is necessary for the argument you are making, I would have presumed you would have calculated it. Are you saying you haven't? Then how can you claim that the ratio of functional to total sequences is practically zero?

Bill Cole said...

lutesuite
I don't think your argument is correct that life can be build without specific proteins being made.

Proteins need to work with other molecules and proteins. This makes the hypothesis that life has evolved by stochastic processes very unlikely. Even if Axe is off by 10 orders of magnitude it does not help.

Relative to more complex eukaryotic proteins Axe's numbers will most likely underestimate the hill that needs to be climbed.

Try to imagine how a spliceosome with 500 proteins that fit together in shape and charge could evolve by stochastic change. 500k nucleotides that form a molecular machine that can repeatably separate and remove molecular fragments with atomic precision and re assemble the remaining molecules.

Faizal Ali said...

I don't think your argument is correct that life can be build without specific proteins being made.

Why should anyone care what you think, especially since you clearly do not understand the topic you attempt to discuss? For instance:

Try to imagine how a spliceosome with 500 proteins that fit together in shape and charge could evolve by stochastic change. 500k nucleotides that form a molecular machine that can repeatably separate and remove molecular fragments with atomic precision and re assemble the remaining molecules.

You just can't stop committing the lottery fallacy, can you?

judmarc said...

How do you evolve a living organism when you evolve a group of proteins with no specific function?

Oy. [Headshake.]

Yeah, how can chemistry happen if God doesn't tell the electrons where to go? And how can apes evolve into humans without God telling all the proteins just how to change? After all, there are so many different ways they could change....

From the lottery fallacy right into the teleology fallacy.

As Allan Miller said above, "the more subfunctionalisation, kinetic tuning and conformational subtlety available to proteins, the less they can evolve. This is clearly nonsense."

Or to put it quite simply, think about this for one second, Bill: Is it true that the more career options are open to you, the less chance you'll be successful? Why not?

Bill Cole said...

lutesuite
"
Try to imagine how a spliceosome with 500 proteins that fit together in shape and charge could evolve by stochastic change. 500k nucleotides that form a molecular machine that can repeatably separate and remove molecular fragments with atomic precision and re assemble the remaining molecules.

You just can't stop committing the lottery fallacy, can you?"

Do you have an explanation how a stochastic process can build this machine?

Faizal Ali said...

The process is called "evolution". I suspect you may have heard of it. Whether that process can properly be considered "stochastic", I don't know. That is irrelevant to the question at hand. You need to demonstrate that the process of evolution cannot produce such a structure. Please show your work.

Bill Cole said...

lutesuite
"The process is called "evolution". I suspect you may have heard of it. Whether that process can properly be considered "stochastic", I don't know. "

Since my argument is that we cannot explain life through stochastic mechanics we have reached agreement.

I agree that evolution can occur.

Faizal Ali said...

I don't see how you conclude we are in agreement. I accept that proteins have arisen thru evolution. If evolution is a stochastic process, then stochastic processes can explain life as it exists today. If evolution is not a stochastic process, then the question remains unanswered. Neither leads to the conclusion "we cannot explain life through stochastic mechanics."

So I take it you are unable to show the data that leads to your conclusion that evolution cannot produce something like the spliceosome. Is it just a faith-based belief of yours?

Bill Cole said...

lutesuite
"
So I take it you are unable to show the data that leads to your conclusion that evolution cannot produce something like the spliceosome. Is it just a faith-based belief of yours?"

This is not my argument.

Faizal Ali said...

Oh. So what is your argument.

Bill Cole said...

It is very unlikely that life evolved through stochastic processes.

Since you are not sure if the evolutionary process is stochastic then we are close enough.

Faizal Ali said...

We are not close at all.

You have to first demonstrate that evolution is a stochastic process. My understanding is that, while evolution in part involves stochastic processes, evolution as a whole is not stochastic. But I welcome input from more knowledgeable members here.

judmarc said...

It is very unlikely that life evolved through stochastic processes.

Jacques Monod, a Nobel prizewinner sometimes called "the father of molecular biology," wrote an essay entitled "Chance and Necessity." Understand his title and you'll have the answer as to whether evolution is (purely) a stochastic process.

Faizal Ali said...

Thank you, more knowledgeable member. :)

judmarc said...

more knowledgeable member

As John Wayne once said, "Not hardly." :-)

Larry Moran said...

Bill Cole says,

Try to imagine how a spliceosome with 500 proteins that fit together in shape and charge could evolve by stochastic change. 500k nucleotides that form a molecular machine that can repeatably separate and remove molecular fragments with atomic precision and re assemble the remaining molecules.

There are five snRNAs required for splicing: U1, U2, U4, U5, and U6. Their lengths vary from species to species but a typical combined length for all five RNAs is about 730 bp. Bill Cole says it's 500,000 bp. He's off by almost three orders of magnitude.

This isn't bad for a creationist since most of them do much worse.

The number of proteins required for spliceosomal splicing also varies from species to species but a typical number is about 80 important proteins. Bill Cole says there are 500 proteins. His value is off by less than an order of magnitude. This is close to perfection by creationist standards.

Bill Cole says that the splicing reaction is incredibly precise. In fact, it is quite error prone compared to other biochemical reactions. The accuracy of splicing a single intron is no better than about 99.9%, which means that the spliceosome machinery makes one mistake for every 1000 splicing reactions.

Bill Cole seems to think we have no idea how the spliceosome and its ancillary reactions could have evolved. In fact, we have a pretty good understanding of how it could have evolved from a group II intron.

Several scientists have developed convincing arguments for the evolution of complexity, especially the spliceosome, by accidental processes that have little to do with positive natural selection. This isn't exactly "stochastic" but it certainly isn't design.

Faizal Ali said...

Thank you, other more knowledgeable member (and gracious host). :)

Bill Cole said...

Larry

Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method
Klaus Hartmuth*†, Henning Urlaub*†, Hans-Peter Vornlocher*†‡, Cindy L. Will*, Marc Gentzel§, Matthias Wilm§, and Reinhard Lu ̈ hrmann*¶

In this 2002 paper greater 200 proteins had been identified in the mammalian spliceosome. If we assume no proteins have been identified since we can assume 200. So reality is in between your number and my number.

You say that your number is how many important proteins evolved. How has importance been determined?

"There are five snRNAs required for splicing: U1, U2, U4, U5, and U6. Their lengths vary from species to species but a typical combined length for all five RNAs is about 730 bp. Bill Cole says it's 500,000 bp. He's off by almost three orders of magnitude."

What about the DNA sequences required to transcribe the spliceosome proteins?

"Bill Cole says that the splicing reaction is incredibly precise. In fact, it is quite error prone compared to other biochemical reactions. The accuracy of splicing a single intron is no better than about 99.9%, which means that the spliceosome machinery makes one mistake for every 1000 splicing reactions."

99.9% for atomic level precision is not precise?

"Several scientists have developed convincing arguments for the evolution of complexity, especially the spliceosome, by accidental processes that have little to do with positive natural selection. This isn't exactly "stochastic" but it certainly isn't design."

I would be interested to read this explanation. Other papers I have read on type 2 intron evolutionary theory do not explain the origin of spliceosome proteins.

What are the accidental processes?

Faizal Ali said...

By all means, continue your impromptu tutorial with Larry, Bill.

But you also need to address the logical fault in your argument, which is in presuming that if organisms currently inhabiting the earth could not have arisen thru "stochastic" processes, then they could not have arisen thru evolution, and were instead designed.

Faizal Ali said...

BTW, Bill, is this sentence the basis of your claim that the spliceosome requires 200 proteins?

To date, >200 spliceosomal proteins have been identified in mammals by MS.

If so, them it's pretty clear what your mistake is, and that it occurs at the level of basic reading comprehension.

Faizal Ali said...

I will just add that, if there are over 200 mammalian spliceosomal proteins, but the typical spliceosome only requires about 80 proteins, that presents serious problems for your core argument that a functional protein can only exist in a single, specific form. Doesn't it?

Bill Cole said...

lutesuite
"But you also need to address the logical fault in your argument, which is in presuming that if organisms currently inhabiting the earth could not have arisen thru "stochastic" processes, then they could not have arisen thru evolution, and were instead designed."

Why do you continue to create a straw-man argument?

Bill Cole said...

lutesuite
Here is a backup paper from 2012.

Spliceosome Database: a tool for tracking components of the spliceosome
Ivan Cvitkovic and Melissa S. Jurica*
+ Author Affiliations

Faizal Ali said...

I'm not strawmanning. I'm trying my best to present your argument based on what you have written. But it's a bit like nailing Jello to the wall. So what did I get wrong? Did you not say your position is "It is very unlikely that life evolved through stochastic processes"? That's a direct quote. And do you not intend this as an argument against evolution?

Faizal Ali said...

Here is a backup paper from 2012.

Spliceosome Database: a tool for tracking components of the spliceosome


OK. So does that tell you how many proteins comprise the average spliceosome? If so, what is the answer?

Bill Cole said...

lutesuite
" That's a direct quote. And do you not intend this as an argument against evolution?"

The argument is simply against the stochastic theories of evolution.

Faizal Ali said...

The argument is simply against the stochastic theories of evolution.

And you accuse others of strawmanning. The irony.

Bill Cole said...

lutesuite
"OK. So does that tell you how many proteins comprise the average spliceosome? If so, what is the answer?"

Do you really want to go through this drill? If it is between 80 and 500 who cares? There are papers that claim as many as 500. The problem for stochastic evolution is the same. If we take Larry's number of 80 "important" proteins and assume 300 AA per protein thats 24k AA's. The number of nucleotides to code for this is 72000. There are 4^72000 possible ways to arrange these nucleotides. These proteins must bind to RNA's and other proteins so they need specific sequences. It is very unlikely this molecular complex was the result of a stochastic process. Also this machine has to duplicate itself several times when the cell divides.

Faizal Ali said...

It is very unlikely this molecular complex was the result of a stochastic process.

It is also very unlikely that it is put together by tiny, invisible pixies. But no one claims it was. So what is your point?

Bill Cole said...

"It is also very unlikely that it is put together by tiny, invisible pixies. But no one claims it was. So what is your point?"

Current evolutionary theory that claims a stochastic mechanism. The lack of a valid stochastic mechanism is a very large paradigm shift from what most people believe.

Faizal Ali said...

Current evolutionary theory that claims a stochastic mechanism.

Such as...?

Larry Moran said...

@Bill Cole

Let's pretend you are truly interested in understanding how the spliceosome evolved.

Is it reasonable to start your investigation with the largest most complex spliceosome you can find or with the smallest, simplest, spliceosome that can do the job? Which one is more likely to provide clues about the origin of the primitive spliceosome?

Faizal Ali said...

I'm not sure that Bill is even aware that there is more than one type of spliceosome. His argument certainly doesn't seem to indicate that he does.

judmarc said...

Bill -

Can you identify the basic probability mathematics error in the following sentence?

"The more ways there are for an event to occur, the less likely it is to happen."

Now have a look at the following sentences by, umm, you:

If we take Larry's number of 80 "important" proteins and assume 300 AA per protein thats 24k AA's. The number of nucleotides to code for this is 72000. There are 4^72000 possible ways to arrange these nucleotides.

Can you identify the same error as in the prior example?

Bill Cole said...

Larry
"Is it reasonable to start your investigation with the largest most complex spliceosome you can find or with the smallest, simplest, spliceosome that can do the job? Which one is more likely to provide clues about the origin of the primitive spliceosome? "

I agree.

Do you have an example of a simple spliceosome to start with? Would yeast be the starting place? How did the first eukaryotic cell evolve given it contained a "simple" spliceosome? How do we evolve introns from prior genes that don't have them?

Bill Cole said...

Here is a paper w the yeast spliceosome protein number.
Likewise, yeast C complexes contained only ∼50 proteins compared to ∼110 in metazoan C complexes. Altogether ∼90 proteins were identified in yeast spliceosomes, nearly all of which have homologs in higher eukaryotes (Fabrizio et al. 2009). Thus, the yeast splicing machinery likely contains the evolutionarily conserved, core set of spliceosomal proteins required for constitutive splicing. Indeed, most of the remaining ∼80 proteins found in human and D. melanogaster spliceosomes have no counterparts in yeast, with many playing a role in alternative splicing, a process that is essentially absent in yeast (Fabrizio et al. 2009).

Faizal Ali said...

OK, Bill. So are you now going to provide the calculations that lead you to conclude that spliceosomes could not have resulted from evolution? After you've addressed the other questions judmarc and I have asked, of course...l.

AllanMiller said...

Why are there cases where eukaryotic mitochondria have linear genomes with eukaryotic telomeres ?

Stockholm Syndrome?

Jmac said...

Diogenes,

I'm not sure where Axe and Gauger made their error, but note that their method necessarily requires mathematical extrapolation, while Szostak's method doesn't. Szostak and co-workers actually created a library of 6 *10^12 random proteins with 80 amino acids and counted how many bound ATP.

Szostak and co-workers actually created a library of random proteins?

I don't think this proves anything especially if you want to prove randomness all the way. You either have to substitute the term or your beliefs.

BTW: How is Szostak doing with his progress on life? Or should I say recopying life that already exists?> From what I know not so good. Maybe you should present him with few pieces of evidence that convinced you that life came about by random, blind processes? He does need it especially if Donald Tramp takes the office. Nonsense research will be cut off.

Denny said...

Larry, I just read - "This anti-science creationist … Pence." I luv ya man, but I think you’re putting words (“anti-science”) in Pence’s mouth. I wouldn’t like you putting those words in my (creationist) mouth.

The stuff of science informs and inspires everyone. Thanks to science, we enjoy, at least in temporal ways, an advanced way of living beyond our ancestor’s wildest dreams. At the same time, our advanced living standard has failed to solve innate human difficulties that have little to do with our worldly home, difficulties that cannot be put to scientific tests. That’s as much a reality as the Sun coming up tomorrow morning.

Evolution theory does make an apparent good model for explaining how things came to be. As a global all-encompassing truth, however, it fails factual verifiability in more ways than can be cited.

In “This anti-science creationist … Pence” post, you omitted two important words. Interpret and infer, which describe a necessary analytical part of the scientific method, and which also give anyone the opportunity to view scientific data differently (to which Pence alluded). Many Evolutionists (not all) interpret scientific findings and infer conclusions through the non-scientific lens/worldview of philosophical naturalism. Others, like Pence (not a scientist), might interpret and infer from what scientists discover through another lens that is free of naturalism and atheism.

The public pays for the progress of science, but not for a small and privileged community of hard working people, blessed to work in the field of natural science, to become masters of our thinking on things tangible (natural science) and intangible (theism and the supernatural). While I personally do not favor teaching scientific origin theories other than Evolution in public schools, I do believe tax-payer supported academic institutions should stimulate and encourage challenges.

I realize that some people could be viewed as anti-science, because they misinterpret the Genesis creation ‘days’ as 24-hour periods. But, I ask this question. On what reasoned basis would anyone oppose competing ideas of how scientific theories should be viewed, especially with the scientific method as a tool and standard for validation?

Diogenes said...

Denny: "you omitted two important words. Interpret and infer, which describe a necessary analytical part of the scientific method"

No. "Interpret" is inserted by creationists in order to make objective facts into opinions. Creationists say (for example) that there are no transitional fossils, then when presented with photos of transitional fossils, they say, "That's your interpretation!" Nope. Ain't buyin it.

Many Evolutionists (not all) interpret scientific findings and infer conclusions through the non-scientific lens/worldview of philosophical naturalism.

Such as? We have the DNA comparisons. We have the fossils. Where "evolution produced the complexity and diversity of life" is concerned, we win. "Lens of philosophical naturalism" has nothing to do with it, evolutionary theory won by the scientific method.

Pence (not a scientist), might interpret and infer from what scientists discover through another lens that is free of naturalism and atheism.

No. Pence is a creationist idiot who would only address evolution by making false statements about it-- not a "different interpretation", but false statements.

Pence also says cigarettes never killed anybody and they don't cause cancer. You gonna call that a "different interpretation" too? Some things are facts, and some people lie about facts.

On what reasoned basis would anyone oppose competing ideas of how scientific theories should be viewed

Competing scientific theories should be compared using the scientific method. Creationism to the contrary invokes God-of-the-Gaps which isn't the scientific method, AND it lies about scientific observations (e.g. "No transitional fossils! Human and chimp DNA are only 70% similar, not 98.7%! Human and dinosaur footprints coexist in Paluxy Texas! Radiometric dating has been debunked!")

You are not at all realistic about how much lying goes into creationism! Every argument against evolution boils down to either statements that are factually false, OR redefinitions of the scientific method, like God-of-the-Gaps. We argue with them all the time. We know how the arguments go.

judmarc said...

I wouldn’t like you putting those words in my (creationist) mouth.

Why not? To contend the Bible can be forced into some Procrustean version of scientific accuracy is ludicrous. If you're going to ignore a couple of centuries worth of confirmed scientific research findings (cross-confirming findings from hundreds of different branches of science, from cosmology to quantum mechanics to geology to biology and on and on), then don't try to duck the necessary implications; wear it frankly. You'd rather believe a couple thousand year old book than results coming out of supercolliders and space satellites. That's fine, but don't try to tell us it's just a matter of interpretation and inference. It's plain refusal of the overwhelming evidence.

Faizal Ali said...

I'm impressed that, Diogenes and judmarc, that you were able to extract enough meaning from Denny's obfuscatory bafflegab to formulate coherent and intelligent responses. Like, what does this mean, even?:

On what reasoned basis would anyone oppose competing ideas of how scientific theories should be viewed, especially with the scientific method as a tool and standard for validation?

Anyone?

Mikkel Rumraket Rasmussen said...

"Homology can well be explained through common design. Thats common practice."

No, it cannot. I have shown this here. Nesting patterns of similarities in the way they exist in living organisms are proof of evolution and a falsification of design, for the logical and philosophical reasons I detail in that post.

Diogenes said...

Lutesuite, it's just the usual "they're closed minded" argument, with creationism referred to as "competing ideas" that are blocked out because of the insufferable strait jacket that we require evidence for it.

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