What is "design" and how to detect it

Loudmouth · Sep 24, 2015

Vaccine said:
You explained how generic information exists in all particles, which was never in doubt. But what makes you think coded digital information is in every molecule? And cite your source.

The same information found in DNA is found in all molecules.

If you think water has syntactic and semantic properties I doubt you understand what these words mean.
The definition of syntactic is relating to the rules of language and semantic is relating to meaning in language or logic.

That is exactly what all molecules have, including H2O. H2O is produced from H2 and O2 using the rules of atomic orbitals and the language of the electroweak forces. We translate the molecules into language:

2H2 + O2 ----> 2H2O

We even see language in single atoms, and it that language is digital. Here is the chart you use to produce the language:

The word for Carbon looks like this:

Of course if we redefine "condensation" to mean "translation" and redefine "reaction" to mean "catalyst", then that makes sense. Resorting to redefining words to make your case only shows how incredibly weak and hopeless it is.

Please show us how DNA is translated (or more precisely, RNA), and show us how it relates to humans reading words.

Show us the actual physical processes.

Well of course it does.

No it doesn't. Simply finding two words in unrelated sentences does not make "specified complexity".

An "increase in binding efficiency" seems like a target to me, unless they painted a bullseye on that after the fact?

The process that introduced mutations was not looking for any target. The selection process occurred after the mutation step, and that was the step which looked for a target.

Actual evolution is evidence of evolution.

Then what would you consider to be actual evolution?

Common design explains all the examples of convergent evolution that fail to fit into a nested hierarchy.

Examples?

Common design also explains all the molecular phylogeny incongruities with a nested hierarchy.

Examples?

With common design genes are viewed as tools in a designer's toolkit. As Meyer points out the pax 6 gene (eyeless) helps regulate development of the eyes in fruit flies, squid, and mice. This contradicts the textbook expectations of Neo-Darwinism and convergent evolution is invoked to explain it.

Convergent evolution can be tested by comparing the sequence of pax6 between species. They should produce the expected phylogenies for nodes that are distantly spaced. Intelligent design makes no such prediction. For intelligent design, there is no reason why mouse pax6 should be more like human pax6 than squid pax6. There is no reason why they should differ at all.

It makes more sense a designer would reuse the same tools in mammals, insects, and cephalopods than the same gene would independently evolve three times.

Where in any reference does it say that pax6 evolved independently three times? All the references I have read say that pax6 was inherited from a common ancestor in all three lineages.

Kylie · Sep 25, 2015

SkyWriting said:
If Jesus were to cause a blind man to see, an autopsy would likely find
his eyes attached to his nerves in a "natural" manner. There is nothing
wrong with the evidence. It's the interpretation of it that is a guess.

"Natural and physical scientists since the 17th century have learned most of what they know about the universe through the scientific method. This method continues to define the way scientists conduct the work of science. It has withstood the test of time.

The scientific method is “a method of research in which a problem is identified, relevant data are gathered, a hypothesis is formulated from these data, and the hypothesis is empirically tested1“ (Table 1). First, the scientist makes an observation or identifies a problem related to that observation. He or she then creates a hypothesis to explain the observation. The hypothesis then allows the scientist to make predictions. The scientist then tests the predictions by experiments or by further observations under controlled conditions.

Falsification is an important element of the scientific method. The scientist ideally attempts to disprove or falsify the hypothesis. If the hypothesis can be disproved, it can then be discarded so that the scientist can move on to a more accurate hypothesis. On the other hand, if experimentation or further observation confirms the hypothesis, this confirmation does not necessarily prove the hypothesis to be true. Other scientists are allowed to test and to attempt to falsify the hypothesis. Repeated confirmations of the hypothesis over time may result in the hypothesis becoming a theory. A theory is a general principle that scientists use to explain phenomena and predict events."

So you take what you can verify, then add an extra step that has no evidence, simply because you hold a particular belief, and then declare this to be the truth?

That's not how to find the truth.

Kylie · Sep 25, 2015

ObamaWoodHollyWood said:
What are the details?

Seriously, can't you spend thirty seconds on Google? https://en.wikipedia.org/wiki/Nebular_hypothesis

SkyWriting · Sep 25, 2015

KTS said:
So you take what you can verify, then add an extra step that has no evidence, simply because you hold a particular belief, and then declare this to be the truth?
That's not how to find the truth.

Then explain your version. Truly, how was this rock formed.....and be true about it.

Waffle Rock West Virginia

AnotherAtheist · Sep 26, 2015

SkyWriting said:
Then explain your version. Truly, how was this rock formed.....and be true about it.

Waffle Rock West Virginia

What's wrong with the following explanation?

http://martinjclemens.com/the-waffle-rock-what-the-heck-is-it/

In my research for this post, I contacted Dr. Jack Epstein of the US Department of the Interior (USGS) to clarify the story about his analysis and to determine the USGS official position on the Waffle Rock formation. I have now received, by mail, a copy of the United States Geological Survey, Department of the Interior fact-sheet on this issue, written by Dr. Epstein in 1977 for the US Army Corps of Engineers, Baltimore District.

This confirms that the story given above, is in fact correct, and that both of the sources for information on the Waffle Rock are based in fact, though both provide only a very basic and condensed version of the facts. A summary of the analysis follows:

As mentioned, the USGS and USACE both take the position that the Waffle Rock and all other examples of such a rock formation are natural and are explained thus: as layers of sandstone were formed during the Appalachian Orogeny (the epoch during with the Appalachian range was formed) approximately 250 million years ago via sediment laid down by ancient streams and water flows, the lower layers of the bedrock experienced compression forces as the Appalachian range heaved and folded. Those different forces, which pushed that lower layer in different directions, resulted in a unique folding of the sandstone into the pattern shown, known as fractures or joints.

“Four sets of joints are apparent in the waffle rock. Sets a and b are roughly perpendicular to each other; sets c and d are at an acute angle to each other. The stress that formed the joints, as well as the folds in the rocks, bisects the angle between joints c and d…”

The mechanism that causes the waffle pattern to appear to be of a different material is similar to that which formed the Klerksdorp Spheres. As the sandstone formed, iron ore particles filtered through the sediment and rock, and possibly leached out of the material below the sandstone, ultimately settling into spaces between sand particles, acting like a cement. Once settled, the compression of the sandstone and fracture stresses turned the iron ore into Hematite (as with the Klerksdorp Spheres), which is darker, harder and of a different consistency than sandstone.

This process is sort of like a perfect storm of conditions, which resulted in the rare but not unique form we see in the Waffle Rock as it sits near Jennings Randolph Lake (also called Bloomington Lake). Another example of the waffle rock sits at the entrance to the US Geological Survey Headquarters in Reston, Virginia. As mentioned in the comment section, there are similar formations in Oklahoma and possibly other locations around the world.

This analysis, as mentioned, comes directly from Dr. Jack Epstein of the US Geological Survey, and stands as the USGS and USACE official position on this strange rock formation. Readers should bear this in mind, when deciding for themselves, just what is the truth. I’ve already heard from several people that the natural formation theory seems unlikely or implausible, but I would suggest that Dr. Epstein and his colleagues are the experts on this particular topic, and perhaps we laymen should defer to their expertise.

My thanks go to Dr. Epstein for his readiness to provide this information.

[1] Dennis, Norm. The Waffle Rock: A big attraction to the thousands of visitors at Jennings Randolph Lake each year. http://www.nab.usace.army.mil/Portals/63/docs/Recreation/JRL/Maps/WaffleRock.pdf

[2] “Jeff” via Robert Weese. Strange Fossil Rock Formation. Rense.com http://rense.com/general3/foss.htm

[3] Webster Bishop, Betty. The Rock and I. ShawWV.com http://www.shawwv.com/betty_bishops_rock.html

Vaccine · Sep 26, 2015

miscicked

Vaccine · Sep 26, 2015

sfs said:
Quoting from the PNAS followup paper from some of the ENCODE folks, "In short, although biochemical signatures are valuable for identifying candidate regulatory elements in the biological context of the cell type examined, they cannot be interpreted as definitive proof of function on their own."

So what? They said as much in the opening statement in the original publication:
"The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/

It didn't mean they weren't able to differentiate between function and non-function. That was part of the discussion of the strengths and weaknesses of the three possible methods to assign function, not a retraction.

sfs said:
I've defined functional as having any effect on any meaningful biological trait. Pretty much the way a human/medical geneticist would: if the sequence composition can affect your health, your strength, your ability to have kids, your looks -- anything you might care about -- then it's functional. The best estimates are that that fraction is around 10% of the genome. Perhaps it's as high as 20%, but there's no way that most of the genome is functional.

This is what they had to say about that method:
"Genetic approaches tend to be limited by modest throughput, although speed and efficiency is now increasing for some methods (36, 38 ⇓–40). The approach may also miss elements whose phenotypes occur only in rare cells or specific environmental contexts, or whose effects are too subtle to detect with current assays."

Why would you insist they use a method that would miss what they were looking for? It seems to me any attempt to limit their search methods makes Darwinian dogma an obstacle to any real scientific discovery.

It's a good thing they don't think that way:
"In contrast to evolutionary (music to my ears) and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease". So while they readily admit their method doesn't identify the function, it's a better tool to provide clues and a launching point for futher studies. By being open to using all 3 methods they demonstrate they are putting the research above any dogma. Going where the fact lead so to speak. They should be commended for their progress, not chastised for thinking outside the box.

Vaccine · Sep 26, 2015

The Barbarian said:
Sorry, analogue, not digital. And almost any string of characters can be "decoded" to have "semantic and syntactic properties." But IDers can't detect them, unless they've agreed in advance if they have it or not. Would you like to put that to a test?

You really should have read the article before coming to that conclusion:

Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer.
http://link.springer.com/article/10.1007/s00018-013-1394-1

Vaccine · Sep 26, 2015

Loudmouth said:
Vaccine said:

It was those views, based on Darwinist presuppositions, that "..for many years REPELLED mainstream researchers from studying noncoding DNA."

Click to expand...

Non-coding DNA is not the same thing as junk DNA. Promoters with known function are still non-coding DNA, but they aren't junk DNA. This is known as a sleight of hand, where you deftly change words without telling the audience that the new word has a different meaning.

No sleight of hand, just a case of you not reading the link:
"Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA."
http://www.sciencemag.org/content/300/5623/1246.short

Vaccine · Sep 26, 2015

Loudmouth said:
The ENCODE definition of biochemical function includes DNA that has no impact on anything important, just like the trash in your kitchen. It is still disposable DNA.

Using their method of defining function will "..thus providing a launching point to study differentiation and development, cellular circuitry, and human disease."
I suppose you would insist on an evolutionary definition of function? One "essentially blind" to what they are studying.
It's called thinking outside the box. Their research is about progress, not adhering to dogma.

sfs · Sep 26, 2015

Vaccine said:
So what?

So you asked what the source was for the estimate that only 10% of the human genome has a selectable function. I told you. Did you not want your question answered?

They said as much in the opening statement in the original publication:
"The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/

Uh, no. The statement you quote here provided the justification for the ENCODE project: we've got all this DNA whose function we don't know, and now we're going to use a bunch of biochemical approaches to determine the function. What they say in the PNAS article is that these methods are not adequate by themselves to determine whether an element is functional or not.

It didn't mean they weren't able to differentiate between function and non-function. That was part of the discussion of the strengths and weaknesses of the three possible methods to assign function, not a retraction.

It was a significant backpedal from their earlier claims, especially the suggestions they made in interviews and press releases. Everyone in the field knows that. If the methods they used in the earlier paper aren't adequate by themselves to determine whether an element is functional (and that's what not being "definitive proof of function" means), then they can't have differentiated between function and non-function, since they didn't use any other methods.

This is what they had to say about that method:
"Genetic approaches tend to be limited by modest throughput, although speed and efficiency is now increasing for some methods (36, 38 ⇓–40). The approach may also miss elements whose phenotypes occur only in rare cells or specific environmental contexts, or whose effects are too subtle to detect with current assays."

Why would you insist they use a method that would miss what they were looking for? It seems to me any attempt to limit their search methods makes Darwinian dogma an obstacle to any real scientific discovery.

No one is suggesting that they limit their search methods. What we're suggesting is that they not make unfounded claims based on methods that cannot support their conclusion. And what I'm suggesting to you is that you stop claiming that most of the genome has been established as being functional (in any ordinary sense of that word), since that isn't the case.

It's a good thing they don't think that way:
"In contrast to evolutionary (music to my ears) and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease". So while they readily admit their method doesn't identify the function, it's a better tool to provide clues and a launching point for futher studies. By being open to using all 3 methods they demonstrate they are putting the research above any dogma. Going where the fact lead so to speak. They should be commended for their progress, not chastised for thinking outside the box.

Oh, balderdash. Biologists are open to using all three methods, and in fact we use ENCODE data all the time in our lab precisely to help identify elements that may be functional.

Vaccine · Sep 26, 2015

Loudmouth said:
The same information found in DNA is found in all molecules.

The question was to explain how. Restating the same baseless claim is not an explanation. Also, I asked for a source to substantiate that claim. Since you're obviously dodging the issue I'll take that as a tacit admission you're just guessing.

Loudmouth said:
That is exactly what all molecules have, including H2O. H2O is produced from H2 and O2 using the rules of atomic orbitals and the language of the electroweak forces. We translate the molecules into language:

Water is a language, really? That you would resort to such tactics as asserting a "language" of the electroweak forces demonstrates just how far you're willing to go to avoid acknowledging truth.

Loudmouth said:
Convergent evolution can be tested by comparing the sequence of pax6 between species. They should produce the expected phylogenies for nodes that are distantly spaced. Intelligent design makes no such prediction. For intelligent design, there is no reason why mouse pax6 should be more like human pax6 than squid pax6. There is no reason why they should differ at all.

Exactly, the expected results are distant species should have dissimilar genes. Except they don't:
"Both eyes use phylogenetically related forms of opsin as their primary photodetection molecule, and an important regulatory gene, pax6, has been found in both vertebrates and some cephalopods, although not in octopus. The use of homologous genes to build nonhomologous structures may lie at the heart of understanding eye evolution and evolutionary processes more generally."
http://redwood.berkeley.edu/bruno/animal-eyes/fernald-science06.pdf
Using similar genes to build different structures in phylogenetically distant species is not expected in a Darwinian view, it is expected in intelligent design theory. Like using standard nuts and bolts in boats, refrigerators, and a crane.

The Barbarian · Sep 26, 2015

Using similar genes to build different structures in phylogenetically distant species is not expected in a Darwinian view,

Actually, Darwin discussed that very thing in his chapter on rudimentary organs. Perhaps it would be a useful thing to learn wnat Darwinian theory actually says.

it is expected in intelligent design theory

Except when we see entirely different things doing the same function, (real scientists call them "analogous organs", and they are a complete mystery to IDers) like the wings of bats, birds, and pterosaurs, or the eyes of vertebrates and cephalopods (the former are made of brain tissue, and the latter are made of epiderm).

SkyWriting · Sep 27, 2015

AnotherAtheist said:
What's wrong with the following explanation?

I asked for the answer, not a speculation because you don't like the fossilized lizard skin explanation.

rjs330 · Sep 27, 2015

Loudmouth said:
I think we have found yet another creationist who can't tell the difference between homology and analogy.

Wait a minute. If evolution were true then we all including plants came from a common ancestor correct? At some point atoms molecules or whatever splint into something different and branched off into different living things be it plant or animal. This whole discussion is ludicrous. This discussion is PROOF that God created all it. Why? All of you who argue for no God and no creation prove the existance of both. The intracasies of life and all those incredible scientific things you bring up are so complex and so intricate and work together is such an impossible fashion to make life work and intelligent life to exist which is PROOF that there was a design for such to exist. The odds of such happening by chance are so great that if it were anything else but God and creation all you who believe in chance would scoff at it. You would all be pointing at the impossible odds and calling us all fools for believing such nonsense. Instead God has the answer of you. And I don't take any joy from quoting scripture and I am not trying to be mean. But these ARE the words from God not me.

A fool in his heart says there is no,God.

Because what may be known of God is manifest in them for God has shown it to them. For since the creation of the world the invisible attributes are clearly seen being understood by the things that are made even his eternal power and Godhead so that they are without excuse.

You my friend seen things VERY clearly where it comes to life and it's workings. Yet you refuse to believe your very eyes that such an unbelievable interworking of such a thing is a matter or design and instead choose to believe in chance.

Loudmouth said:
I think we have found yet another creationist who can't tell the difference between homology and analogy.

Wait a minute. If evolution were true then we all including plants came from a common ancestor correct? At some point atoms molecules or whatever splint into something different and branched off into different living things be it plant or animal. This whole discussion is ludicrous. This discussion is PROOF that God created all it. Why? All of you who argue for no God and no creation prove the existance of both. The intracasies of life and all those incredible scientific things you bring up are so complex and so intricate and work together is such an impossible fashion to make life work and intelligent life to exist which is PROOF that there was a design for such to exist. The odds of such happening by chance are so great that if it were anything else but God and creation all you who believe in chance would scoff at it. You would all be pointing at the impossible odds and calling us all fools for believing such nonsense. Instead God has the answer of you. And I don't take any joy from quoting scripture and I am not trying to be mean. But these ARE the words from God not me.

florida2 · Sep 27, 2015

rjs330 said:
This isn't hard at all.

Isaiah 42:5-6 This says God the Lord who created the heavens and stretched them out who spread out the earth and what comes from it, who gives breath to the people on it and spirit to those who walk in it: I am the Lord; I have called you to righteousness; I will take you by the hand and keep you; I will give you as a covenant for the people and a light for the nation's,

Heb. 1:10 An you Lord laid the foundation of the earth in the beginning and the heavens are the work of your hands

Romans 1:20 For his invisible attributes namely hisveternal power and divine nature have been clearly perceived ever since the creation of the world in the things that have been made so they are without excuse.

God created everything and preserves everything. His nature is bound up creation and the laws of the universe which he set in motion. The wind blows cause God created it to be so. The seas provide water by the laws of evaporation because h3 created it to be so. The seas don't overwhelm us because God placed the moon in the heavens to be at the precise location to provide the perfect amount of gravity. There is so much that proves the existence of God in nature by natures design that it's sad you refuse to see it. So you are without excuse.

So when thousands of innocent men, women and children are killed every year in natural disasters - did God get distracted or something? You say the wind blows because of God so therefore natural disasters are because of God. That means that either he takes his eye of the ball (unlikely if he is omnipotent and omnipresent) or that God consciously chooses to kill all those innocent people each year. Either way, your version of God doesn't sound very loving.

Kylie · Sep 28, 2015

SkyWriting said:
Then explain your version. Truly, how was this rock formed.....and be true about it.

Waffle Rock West Virginia

First of all, the fact that there is no readily apparent alternative cause does not mean that "Goddidit" is the best answer.

Secondly, there are any number of natural causes of orderly patterns in rocks. I would suspect something similar happened here.

Loudmouth · Sep 28, 2015

Vaccine said:
No sleight of hand, just a case of you not reading the link:
"Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA."
http://www.sciencemag.org/content/300/5623/1246.short

Yes, sleight of hand. Noncoding DNA and junk DNA are not the same thing.

Loudmouth · Sep 28, 2015

rjs330 said:
Wait a minute. If evolution were true then we all including plants came from a common ancestor correct? At some point atoms molecules or whatever splint into something different and branched off into different living things be it plant or animal.

Animals are eukaryotes. Plants are eukaryotes. Their common ancestor was a eukaryote. They are still the same living things, with modifications.

The intracasies of life and all those incredible scientific things you bring up are so complex and so intricate and work together is such an impossible fashion to make life work and intelligent life to exist which is PROOF that there was a design for such to exist.

Argument from incredulity.

The odds of such happening by chance are so great that if it were anything else but God and creation all you who believe in chance would scoff at it.

Reference to non-existent odds. If you are going to reference odds, please show us your math.

Loudmouth · Sep 28, 2015

Vaccine said:
The question was to explain how.

The information contained in DNA is encoded by its chemical and physical interactions as part of its chemical makeup. The same for water.

You also showed how humans "translate" DNA into human letters. The same for water. We express it as H2O. We also use human letters and numbers to describe single atoms.

Water is a language, really?

H2O. That's the language. It has letters and everything.

"Both eyes use phylogenetically related forms of opsin as their primary photodetection molecule, and an important regulatory gene, pax6, has been found in both vertebrates and some cephalopods, although not in octopus. The use of homologous genes to build nonhomologous structures may lie at the heart of understanding eye evolution and evolutionary processes more generally."
http://redwood.berkeley.edu/bruno/animal-eyes/fernald-science06.pdf
Using similar genes to build different structures in phylogenetically distant species is not expected in a Darwinian view, it is expected in intelligent design theory. Like using standard nuts and bolts in boats, refrigerators, and a crane.

What happens when we compare the sequences for those genes? Does it produce the expected phylogeny?

What is "design" and how to detect it

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