Friday, December 18, 2009

Got Junk?

Atheists tell us that one way of knowing whether what you are doing is “science” is, “Is it testable?” Does your method of inquiry include making a prediction and then seeing if your hypothesis will fulfill that prediction. For those who believe that only science can reveal truth, this is a VERY important step.

Intelligent Design theory follows this route. Before I get to that, let me point out a couple other areas that the scientific concept of ID covers.

. The case for ID is based on empirical evidence. I’ve given you almost two weeks of empirical evidence beginning with the first post called, “Nothing Did It.” This same post gives an example of the digital code that is found in every cell of every living object. As well, ID examines irreducible complexity of molecular machines as well as the circuits in all living cells. ID examines the pattern and order of appearance of groups of organisms in the fossil record. ID investigates the fine tuning of the universe and the constants and qualities and laws of physics. Not only the information storage capacity of DNA but the decoding and transmitting system of Proteins is examined in ID. Intelligent Design is, at it’s base, founded on the commonly accepted observations of the world around us.

For the most part, the majority of the posts in this series have been an example of one means of testing in ID. That is, testing the causal adequacy of competing hypothesis. Darwin himself used this method. Oooo. As a result, we saw, or at least those willing to see, found that ID explains better than Chance, Chemical Necessity and RNA reproduction the interdependent information processing system that is found in each and every living cell.

Acceptance or rejection of competing theories is made based upon what we know from experience. ID is not just a known cause of large quantities of specified complexity. ID is the ONLY known cause of large quantities of specified complexity. That means ID theory fulfills two important scientific criteria; that of causal adequacy (It can do the job) and causal existence (It has done and is doing the job).

Back to predictions. Let’s compare material evolutionary prediction and ID prediction on one important area. That area is junk DNA. I doubt that’s a new term to anyone commenting here so I won’t go into a lengthy explanation. In short, however, junk DNA is DNA that doesn’t code for proteins, as does the DNA we’ve all come to know and love.

As you might guess, those who believe that cells have arisen by trial and error predict that there should be a lot of, well, leftover junk. This is useless stuff that a trillion years or so ago would have been a brand new idea and as good as cells got back then.

Michael Shermer says, “Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragmented copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.”
“Why Darwin Matters” 75

“The critics of evolution like to say that the complexity of the genome makes it clear that it was designed. But there’s a problem with that analysis, and it’s a serious one. The problem is the genome itself; it’s not perfect. In fact, it’s riddled with useless information, mistakes, and broken genes. Molecular biologists actually call some of these regions ‘gene deserts,’ reflecting the barren nature.”
Ken Miller, “Only a Theory” 96-97

“If you were designing the genomes of organisms, you would not fill them up with junk.”
Philip Kitcher, “Living with Darwin” 57

There’s more of this kind of thing, but you get the idea. Junk - waste products and such are exactly what natural selection predicts with regard to the genome.

Not so with Intelligent Design. ID predicts that most of the non coding sequences in any genome should perform some biological function. That’s not to say that there won’t be any broken or degraded DNA. Remember, Intelligent Design does not deny evolution or natural selection. What ID predicts, however, is that functional DNA should far out number nonfunctional DNA.

. Evolution of the first cell predicts a lot of junk DNA.

. ID of the first cell predicts a minimal amount of useless DNA.

What is now known is that the non coding DNA, formerly thought to be junk by evolutionists, actually performs a massive amount of important biological functions - just as ID predicts.

Remember this line, from the atheist Keith? “If we [atheists] find evidence to show something we thought was wrong, we don't hold on to the original belief like leach.” Ya, right.

Just as Stanley Miller’s faux experiment re: amino acids forming in early earth’s reducing atmosphere remained on the books long after it was known to be wrong, Shermer, Miller (Kenneth) and Kitcher have continued to spread the predictions and the false “confirming findings” re: junk DNA long after it’s been known that their predictions and their theory was wrong. How wrong are they?

Non coding or junk DNA:
. Regulates DNA replication
. Marks sites for programmed rearrangements of genetic material
. Regulates transcriptions
. Controls the interactions of chromosomes with the nuclear membrane
. Influences the proper folding and maintenance of chromosomes
. Controls RNA processing, editing and splicing
. Modulate translation
. Regulates embryological development
. Repairs DNA, and
. Aids in immunodefence
Meyers, 407

This is a long, long way from being junk as natural theories of evolution predicted.

It’s bang on as ID predicted.

17 comments:

Hugo said...

(Again, commenting on the most recent post even if it's related to another)

Makarios: What is the origin of the code? If I understand you correctly, what I call a code really isn’t a code. It’s just, um, material?

Yes, I think you got it.

Obviously, you are not going to drop ID right away because of that... but you do have your answer right there; there never was any code, it's just an illusion.

Nothing to add for now, please consider that carefully.

Makarios said...

An illusion, like the concept of "I"?

And regardless of the evidence that I presented, Chance and Chemical Necessity and RNA replication are all workable scenarios?

There's no reason to doubt that this is how the informaation / instructions (are we allowed to call it that) in the cell developed?

Makarios said...

Hugo: I know you've been busy and I do appreciate the time and effort you put into explaining to me what Richard Dawkins says, but, did you read my post "Huh?"

And if so, could you tell me one last time how Richard Dawkins would respond?

Ginx said...

I can confidently stop reading after "Atheists tell us..."

Makarios said...

Well Ginx, the people who continually tell me scientific stuff are not in fact scientists.

They criticise what I say as though they're ARE scientists, but in reality, their only common denominator is that they are all, to a person, atheists.

JD Curtis said...

They criticise what I say as though they're ARE scientists

Sort of. They're more like people who are locked into a worldview in which methodoligical naturalism is THE ONLY EXPLANATION that is possible for origin of life discussions. The only problem is, their presupposition is just that, rather than anything resembling an actual conclusion.

So far so good though. Nobody is trying to change the topic to Young Earth Creationism as of yet. Bravo.

scripto said...

"ID examines irreducible complexity of molecular machines as well as the circuits in all living cells. ID examines the pattern and order of appearance of groups of organisms in the fossil record. ID investigates the fine tuning of the universe and the constants and qualities and laws of physics. Not only the information storage capacity of DNA but the decoding and transmitting system of Proteins is examined in ID. Intelligent Design is, at it’s base, founded on the commonly accepted observations of the world around us."

That's a lot of examining based on other people's research. Where's the published research resulting from all this examination? What particular structures have been predicted to have been designed and when? What is the purported mechanism? What specific structures have been deduced as being specifically complex using Dembski's filter and who is actually using any of these ideas in research? It's all a shell game based on an inadequate analogy. When you look into ID there is really nothing there.

Makarios said...

JD: I just find this all so sad. Plus at this time of year my counselling workload it trough the roof and, well, thanks for your support at least.

Script: You raise some good points.

I've got two kids in two different hockey games tonight in two different towns. That means that I'm busy.

I don't know you at all so, it's not fair of me to lump you in with all the other atheists who raise points but who aren't really interested in any answer that does't follow the party line. And when they do get an answer they can't ignore (see post "Correct Me"), they just change the rules or change the question or talk about Noah's Ark - Anything will do as long as they don't have to stay on topic. Hope you're different. Regardless, I will get back to you.

Hugo said...

An illusion, like the concept of "I"?

You mean the mathematical "i" or the "self"?

And regardless of the evidence that I presented, Chance and Chemical Necessity and RNA replication are all workable scenarios?

Chance? Yes, but not lottery-style. Chemical Necessity? If you mean biochemical natural laws, yes. RNA replication? No, I don't think so, that's too complex already I would say. I see no reason to think that the first self-replication molecules were something like modern RNA.

There's no reason to doubt that this is how the informaation / instructions (are we allowed to call it that) in the cell developed?

Doubting is always very sane in my opinion. And yes I think that it does make sense to call it information/instruction; but it's just a shortcut we use when talking among us. It's like when we say that giraffe were designed to get leaves on high trees, or dauphins were designed to be fast swimmers, or bees designed pretty flowers. Nobody literally means designed, just like nobody literally means information or instructions.

Hugo said...

Hugo: I know you've been busy and I do appreciate the time and effort you put into explaining to me what Richard Dawkins says, but, did you read my post "Huh?"

And if so, could you tell me one last time how Richard Dawkins would respond?


Ya I had read it already. I cannot answer for Dawkins, I am not qualified enough, but I can tell you what I think of that post, and use Dawkins' approach, because it goes back to what I consider the basic problem in your defence of intelligent design: the illusion of information planted in the cell as is.

You give an example of letters representing genetic codes and ask: Do you think it took intelligent thought to construct this information in a manner that would allow for life to begin to exist? and the answer is simply no, because you see it backward.

Like Dawkins says in his book, when we look at evolution, we are like detectives who arrive at the scene of a crime, long after the act. Therefore, we cannot see the code you present being built, we can only see it as it is right now, and try to explain how it got there.

When you suggest ID as an explanation, you basically explain nothing; all you can say is that this particular code is so specific that it must have been designed to be that way. This does not explain why, how, when. It only shows the incredulity of the observer in front of such a wonderful mechanism.

What the naturalistic explanation would present is something more like: there was in nature all these different arrangement of "letters". The ones that were useful for something, allowing the copy of a particular set of molecules perhaps, were kept because of the advantage they provided to the other molecules that had this arrangement of "letters".

So yes, it is a chance in my opinion that kick started the first replication, but as I mentioned at the beginning, it's not lottery-style chance, in the sense that all the possibilities were there at first, and then only the useful ones were kept, and that is not chance at all. It's not that suddenly the perfect code arose by chance, quite the contrary. Chance modifications allowed the existence of every possibility, or most of them, and then the non-random process of natural selection favoured the most useful components to go on.

I am afraid that this still does not explain the precise beginning of life, but that's not my goal as I have not enough knowledge to do so. My point is that there is absolutely no evidence pointing to a design, or a specific pattern, that would have been set in place as is. Everything in the natural world is made from simpler natural parts that tend to associate themselves according to natural principles that we understand more and more every day. Arguing that a particular components is too specific, or too complex, or both, to be considered natural is a case of special pleading, or an argument from ignorance when the evolution of the so called specified complex parts have already been explained.

Just to make sure, no, I am not ignoring all the arguments you propose in favour of ID; it's just not conclusive. I could be wrong, but that would be my opinion, and there are scientists who I trust much more than myself who would not even allow the possibily of being wrong, so I guess I prefer to listen to them...

Thanks for your time Mak,

Christmas Office Party time!! YEAH!!
Have a nice weekend...

Gorth Satana said...

About "Correct Me!".
You had already been given the answers to those questions. I gave you a few non-biased links. You either didn't read them or didn't understand them.
I thought you were just being "obstructionniste".

It like if I argued that cars were a conspiracy because I knew all cars could fly. You smile and point to the wikipedia page for cars. I restate that cars fly. I use a ludicrous source of information like a comic book. I use the "fact" of flying cars to "prove" a conspiracy.
You ask if I've read the wiki page and give a few reasons why all cars don't fly. I restate that all cars can fly. You link to mechanics who say cars can not fly. I say there is a conspiracy and the mechanics know that cars can fly. I pepper my response with insults. I use logical fallacies to prove they can't NOT fly. You point out the fallacies. I reprint my post and say no one has posted any serious responses so cars all fly.
Now imagine this happening over and over. Every day. Eventually you say to yourself, "Ah, forget it, he has a overwhelming psychological to believe in flying cars because he wants to fly one into the sky one day. If he wants to believe that cars fly and nearly one hundred percent of mechanics are involved in a conspiracy, no amount of information will sway him."
I then declare victory.

Gorth Satana said...

I thought you were just being "obstructionniste".

In English it's called "passive aggressive".

Ginx said...

First of all, who is "us?" You got a turd in your pocket? Second, scientists will tell you that if you asked them or if you read what they write. Third, the tone is so condescending I don't have to read another word because you telegraph your intent. It's "us vs. them," as defined by Romans 8:31

Makarios said...

Scripto:

First of all, I’m going to pre judge you. If you find it offensive - move along. I’m going to a lot of work to answer your objections and I fully believe that once they’re answered, you’ll just move the markers, redefine the question or some such nonsense.


You said:
“That's a lot of examining based on other people's research.”

What’s wrong with that? You don’t think everyone does original work do you? That’s one of the humorous things about talking to atheists. I’m mocked for presenting other people’s thoughts and it's done in a manner that suggests that all the comments of atheists are completely original. Sometimes you guys are such a joke.
=================
“Where's the published research resulting from all this examination?”

Ah, yes. Peer review. The atheists prize demarcation. I don’t know how I could find all of them but I know of a few.
. Holden, “Random Samples”

. Giles, “Theory of Intelligent Design”

. Klinghoffer, “The Branding of a Heretic”

. Powel, Intelligent Design”

. “Brief of Amicus Curiae”

. Behe, “Darwin’s Black Box”

. Gonzalez and Richards, “The Privileged Planet”

. Thaxton, Bradley, and Olsen “The Mystery of Life’s Origin”

. Dembski, “The Design Inference”

. Campbell and Meyer, “Darwinism, Design and Public Education”

. Dembski and Ruse “Life’s Origin

. Minnich and Meyer, “Genetic Analysis of Coordinate Flageller and Type III Regulatory Circuits

. Dembski, “Mere Creation”

. Barrow and Tipler, “Anthropic Principle vs. Divine Design”

. Behe, “Self-Organization and Irreducibly Complex Systems”

. Wells, “Do Centrioles Generate a Polar Ejection Force?”

. Behe and Snoke, “Simulating Evolution by Gene Duplication”

. Dembski and Marks, “The Conservation of Information; Measuring the Information Cost of a Successful Search”

. Voie, “Biological Function and the Genetic Code are Independent”

. Davison, “A Prescribed Evolutionary Hypothesis”

. Lonnig and Saedler, “Chromosomal Rearrangements and Transposable Elements”

Now here’s the scenario that I anticipate.

Atheist: “There aren’t any peer review papers because ID isn’t science. It’s just a shell game. What? Oh crap! I didn’t know there were peer review papers for ID. Well there shouldn’t be any peer reviews because ID isn’t science.”
==============

Makarios said...

Cont'd:
“What particular structures have been predicted to have been designed and when?”

. No undirected process will demonstrate the capacity to generate 500 bits of new information starting from a non biological source.

. Informational accounting will reveal that sources of active information are responsible for putatively successful computer-based evolutionary simulations

. Future experiments will continue to show the RNA catalysts lack the capacities necessary to render the RNA-world scenario plausible.

. Informational accounting will reveal that any improvements in replicase function in ribozymes are the result of active information supplied by ribozyme engineers.

. Investigation of the logic of regulatory and information processing systems in cells will reveal the use of design strategies and logic that mirrors (though possibly exceeds in complexity) those used in systems designed by engineers.

. Cell biologists will find regulatory systems that function in accord with a logic that can be expressed as an algorithm.

. Sophisticated imaging techniques will reveal nanomachines in centrioles that play a role in cell division. Other evidence will show that malfunctions in the regulation of these machines are responsible for chromosomal damage.

. If ID played a role in the origin of life, but not subsequently, prokaryotic cells should carry amounts of genetic information that exceed their own needs or retain vestiges of information-rich structures that exceed the causal powers of chance, necessity, or the combination of the two.

. If a designing intelligence acted discretely in the history of life, the various subdisciplines of biology should show evidence of polyphyly.

. The fossil record, in particular, should show evidence of discrete infusions of information into the biosphere at episodic intervals as well as a top-down, rather than bottom-up pattern of appearance of new fossil forms.

. If an intelligent (and benevolent) agent designed life, then studies of putatively bad designs in life, such as the vertebrate retina and virulent bacteria - should reveal either (a) reason for the designs that show a hidden functional logic or (b) evidence of decay or originally good designs.

. If the flagella motor was intelligently designed and the type-3 secretory system devolved from it, the genes that code for the bacterial flagellar motor should be older than those that code for the proteins in the T3SS, and not the reverse. Alternatively, if the T3SS and the flagellar motor arose by design independently, T3SS should have unique (nonhomologous) genes that arenot present in the genome for the flagellar motor.

. The functional sequences of amino acids within amino acid sequence space should be extremely rare rather than common.
================
“What is the purported mechanism? What specific structures have been deduced as being specifically complex?”

I’ve answered that in this series of posts. It’s begins with “Nothing Did It.”

scripto said...

Sorry to comment and run. Blizzard. I had to shovel snow instead of...well, you know

"Atheist: “There aren’t any peer review papers because ID isn’t science. It’s just a shell game. What? Oh crap! I didn’t know there were peer review papers for ID. Well there shouldn’t be any peer reviews because ID isn’t science."

All evolutionists are atheists? - must be news to Collins and Miller (and me). Most of those papers you site are not peer reviewed in the appropriate journals. Those that are deal with a specific area of evolutionary theory that may or may not be called into question by their conclusions. In no case do they offer ID as a supportable alternative. And in no case have they made any headway in biological journals. I'm looking for independent corroboration from someone outside the incestuous glad handing of the Discovery Institute. Any search in pub Med regarding any aspect of evolutionary research, no matter how obscure, turns up more information than the entire output of the ID movement. There is no evidence for ID. You act as though Dembski's specified complexity and Behe's Irreducible complexity are some sort of fait accompli simply by definition. But Dembski has not defined his terms to satisfy any statiticians or information theorists and has applied it to no biological structures. Behe IR is found wanting at any level where it is applied. He keeps backtracking through more and more specific parts of a generalized structure. So molecular machines are irreducible complex components of larger irreducibly complex structures? Please. It is fundamentally useless as an idea. Your 500 bits of info idea sounds nice and sciency but until the terms are better defined and it gains some sort of traction among people who know what they're talking about (sadly, not I) it remains a non starter. ID is backwards science, searching for evidence for a predetermined conclusion. It is a dishonest enterprise. What structures were designed? Where is the historical timeline? Where is the proposed mechanism? Without these, we are not even talking about the same thing let alone a competing theory.

Makarios said...

Merry Christmas Scripto - Good luck on your journey.