Why not God of the Gaps?

@RichardG

Just to give another example of what biologists are seeing.

Most genes in vertebrate genomes have introns. These are long stretches of DNA that are clipped out of the RNA transcript from that gene. The exons in a gene contain the coding regions that are ultimately translated into protein.

image

The vast majority of DNA sequence within introns doesn’t affect its function. The sequence immediately surrounding a splice site matters, and there are a few functional sequences found in introns here and there, but for the vast majority of intron sequence the sequence can be entirely random and still function as an intron since it is spliced out and doesn’t affect the resulting coding sequence.

Knowing this, what would we expect to see if common ancestry and evolution is true? First, we would expect mutations to happen in both exons and introns. However, mutations that occur in exons will have a much, much higher chance of being deleterious and will therefore be selected against by natural selection. Since the DNA sequence doesn’t matter for the vast majority of intron sequence, very few deleterious mutations will occur in intron sequence. This means we would expect exons to accumulate fewer mutations over time than introns. This means we would expect to see more differences in intron sequences when we compare the same gene between two distantly related species. We would also expect this difference to increase with evolutionary distance.

Guess what? This is exactly what we see (click for larger version).

This was downloaded from the UCSC genome browser, and the gene we are looking at is human mmp9, a gene shared by a wide range of vertebrates. The boxes are the exons, and the line connecting the boxes are the introns.

Below the gene is a graph showing sequence conservation across 100 different vertebrate genomes. The higher the line goes the more sequence conservation there is. Notice how the graph spikes where there is exon sequence, and flatlines where there is intron sequence.

There are also a few model vertebrate species listed below. Where there is black there is matching sequence. Notice how the entire bar is black across the chimp genome. Again, a close relative of humans has sequence very similar to humans. However, as you increase evolutionary distance you will notice that there are fewer and fewer similarities in the intron sequence while there is still noticeable sequence similarity in the exons. When you get to the zebrafish and frog (Xenopus tropicalis) the only sequence similarity that can be consistently found is in the exons.

This is EXACTLY what we would expect from evolutionary mechanisms. I have yet to see anyone explain this data outside of evolution. For example, if species were separately created then why not use identical introns for fish and humans since the sequence really doesn’t matter? Why should introns differ more than exons if life did not evolve and does not share common ancestry?

note: Inspiration for this post comes from “Faith and the Human Genome” by Dr. Francis Collins. He discusses the same patterns for a different gene.

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Says it all.

You see what you want to. I can do that with Scripture as well.

Doesn’t make me right though

You really didn’t get my argument did you? Its not about the patterns, or the minutia of structure. It is about function. Function trumps all your nesting and familiars.

Ocham’s Razor? The simplest answer is probably correct
(not really what he said but near enough)

Richard

Why? I am not looking for common ancestry.

You tell me what you would expect to see with common building blocks?

Richard

Then explain why I am wrong if you think I am wrong. Please explain why the patterns we see are not the patterns we would expect from common ancestry and evolution.

Your completely uninformed and subjective opinions about function does not trump the objective facts. The reason scientists don’t take arguments like yours seriously is that they don’t address the evidence.

It’s the rule of parsimony.

Notice that the quote is from 1882. For over 140 years the nested hierarchy (i.e. tree of life) has been one of the biggest pieces of evidence for evolution and common ancestry. If you can’t address this evidence then your argument is a non-starter.

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So you haven’t looked to see if there is evidence of common ancestry? You just reject it out of hand without even looking at the evidence?

If there was no common ancestry or evolution then I would not expect to see a nested hierarchy. I would not expect to see more differences in introns than in exons when comparing homologous genes. For example, why not use the same common building blocks for the fish mmp9 gene and the human mmp9 gene? We would only need to change the exon sequence, so why not keep the same exact intron sequence? There is absolutely no reason why I would expect to see such wildly different intron sequence in the human and fish mmp9 gene if they did not share common ancestry and were created separately from common building blocks.

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Just tell me I am wrong about the function of DNA.

Show me how this nested theory performs in the macro world. Show me the progressions or heredity. Show me the developing organisms beyond simple adaption Demonstrate that there is more to this theory than genetic patterns and perceived nested hierarchy. You can’t because the evidence does not seem to exist. Fossils are not detailed enough and you can’t go back in time to watch it happen.

Richard

“In Laymans terms it is a recipe. You want a leg? there is DNA sequece to make it. An Eye, A heart, Digestive juices? Each ne has a DNA sequence.
. . .
DNA is not even the building blocks it is the means of putting blocks together. There will be one basic sequence for bones, another for the shape, another for the connections and so on. A vertebrate will have the same base sequencies.”

That’s wrong. There is no leg gene, heart gene, or eye gene. That’s not how it works. You started with a recipe as an analogy, which can actually be a good analogy, but then you abandoned it right away.

Continuing with your recipe analogy, your pantry, freezer, and refrigerator is the genome. The recipe is the type of cell you want. To make that cell you take different ingredients and mix them in different ways. The ingredients would be genes in this analogy. You may use flour for many different recipes just as the same gene is used to create many different types of cells. You may also have different smaller recipes whose products are combined into a larger dish. This is how organs are created, by a combination of different cells each with their own recipe.

Another decent analogy is an orchestra. Each gene would be a member of that orchestra. A song would have different people playing at different times at different volumes. There is no instrument called “Beethoven’s Fifth”. In the same way, each cell, tissue, and organ is the result of different genes being turned on at different times at different transcription levels. Just as many different songs will use the same instruments, so too do different cell types, tissue types, and organs.

That is all covered in the field of evolutionary developmental biology.

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That’s not true. Neutral means no alteration in fitness at the present time.

Irrelevant – on the chemical level, mutations are mutations.

I can only conclude that you didn’t read the article. Here’s the link again–
Testing Common Ancestry: It’s All About the Mutations - Article - BioLogos

This is really very simple: we can count the numbers of mutations, we can measure the rates of mutations, and we can count the numbers of mutations between a present species and its ancestor and thus make an estimate of the time between that ancestor species and the modern species. Since we can date ancestor species fairly well using geology, we can see if the time difference derived from mutations matches the time difference derived from geology. It turns out that there’s not much deviation, and so we have confidence that we know how much time it took for the ancestor species to give rise to the modern species. And since there’s not much deviation, then yes, we have in fact “measured the sort of change needed for Evolution to do what it claims to”.

Not really. There are some cyclic long-term patterns, but that does not mean that all long-term patterns are cyclic. For example, climate and thus weather patterns changed in non-cyclic ways when the Atlantic broke through at the Straits of Gibraltar and flooded the then mostly-dry Mediterranean basin, and also when the Mediterranean broke through and flooded the Black Sea basin that had had a large freshwater lake. Earlier, non-cyclic climate change occurred when the Isthmus of Panama formed and cut off the Atlantic from the Pacific, when Pangea split and the Atlantic was born, when the Indian plate collided with the Asian plate and the Himalayas began to form. There are others, but these are sufficient to make the point that weather patterns are only cyclic in close terms, not in the long run. Some cyclic influences continue, such as solar cycles and shifts in Earth’s orbit, but the effects of those cycles on the planet’s weather depend on non-cyclic factors as noted above.

It’s entirely the point: if the influence can’t be measured, it is not relevant to science since science is about what can be measured. It will be recorded as data but no more.

Rubbish. I’m pointing out that the information is the same in 3D so your claim it depends on misrepresentation of a 2D diagram was false.

That’s not what the diagrams are showing. They’re showing that there is a set of bones that over time change their shapes and positions, and that these can be and have been tracked, so it’s known that what is now bone x’ (x-prime) used to be just bone x.

No, it wouldn’t, any more than the shape of a river delta is the result of planning. “Beneficial” has nothing to do with planning, it has only to do with result.
Here’s a comparison: consider a card game in which additional cards are provided after each turn in the game. If you have in your hand a sequence of three cards and another of two cards that are separated by just one card, and on the next turn you are dealt that card with the result that you have a sequence of six cards, was the dealing of that card the result of planning? No, unless you maintain that the dealer was cheating!

It is exactly as obvious: you have to verify which publications are reliable and which aren’t. Now that requires checking web pages when back in the day it required checking issues filed in the stacks or on microfilm. The only changes are that the storage method is different and that it’s much easier to get your “publication” into “storage”.

Those are exactly the point: you are misrepresenting or misunderstanding the scientific process in general and evolution in particular.

Um, no, because in this case you’re insisting on something that is not at all true, that “anyone who criticizes evolution is declared a biblical creationist”. Or are you admitting that biblical creationists are drawing conclusions the evidence doesn’t support?

Of course we’re “talking only about how” – that’s the nature of science.

No, science follows the evidence. If there were ever any evidence that “who” is in the least relevant, that would be addressed.

No, that’s where some religious believers force science into conflict with religion, and the irony is that they do so because they have failed to keep up with what is known about scripture – if they’d kept up, there wouldn’t be any YECists running around deceiving Christians.

Fine – but that has nothing to do with science. The moment you start to talk about God you’ve stopped doing science because science is about what can be measured. There is no way to measure or test for God, so God is irrelevant to science.
Here’s an analogy: on Christmas morning a kids opens a toy that has to be assembled. To do the assembly he follows the written directions. The assembly process is the same regardless of whether it was Mom, Dad, Aunt Bertha, Uncle Roscoe, a neighbor, or whomever that gave the toy… The process of science is the same whether God is behind it or not.

Consider a recipe for a cake that happens to include instructions for growing the crops from which the ingredients are made, how to make those ingredients, how to package them, and how to get them to a store where they can be acquired by a baker. What you’re claiming is like that because there is a lot of small details in this recipe that there’s no way to bake a cake.

It’s been done, but apparently you aren’t reading the linked articles where actual scientists address the science.
It comes down to this: either evolution is real, or God is a liar, because the evidence is so overwhelming that no other explanation is viable.

It’s interesting to note that there are companies that make use of DNA to track people’s ancestry, usually in general terms such as what nation an unknown great-grandfather was from, but in some cases tracking down a specific lineage, e.g. answering the question of whether someone is descended from a historical figure for whom DNA is available.
Just the ability to be that specific says two things: first, that it’s not just a matter of common building blocks, and second, that DNA can be used to trace ancestry. After all, if it’s good for five generations or a dozen or a score, it’s also good for five hundred generations or five thousand or five million.

Nice analogy!

That’s already been done: you’d see no apparent relationship between DNA and related species because there are multiple “building blocks” for quite a number of physical attributes so it wouldn’t matter which one got used for a given creature – in other words, if it’s common building blocks, the DNA patterns would be highly random.

And if it were just common building blocks, we’d see a spread of data more like that of the makeup of rocks in geology: no ‘family tree’, just near-random arrays of characteristics.

@richard

It’s annoying that a great deal of this thread boils down to you failing to understand science, failing to understand evolution, failing to understand the implications of your ideas, failing to grasp the explanations you’ve asked for, and repeated requests for information that has already been posted while you repeat things that have been shown to be false. On the face of it, it’s difficult to tell whether this results from an incapability to understand what’s being discussed or whether it’s just a deep lack of respect for others.

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No.ABsolutely not. That is claiming that Genesis is meant to be science. Or that the bible was written by God. Neither is true.
You perptually argue against Genesis not theistic Evolution. Perhaps you do not understand theistic evolution?

You also misunderstand my criticism as if I am trying to ridicule all of Evolution. I do not. But, I see limitations that you do not.
Your analogy about knowing the results because of the ingredients does not work. You are always ignoring complexity. It’s not just knowing the ingredients it is also how to mix them and the necessities of life and living during the process.Just because it happened does not mean you have found the complete method. Evolution is in there, but there are aspects that Science seems to gloss over. And talking genetics does not answer them You cannot suspend life while genetics reorganises the inner workings.
Actual scientists will never even consider the idea that there is a designer. We both know this, but to claim heredity on a mathematical basis is just cloud cuckoo land. Yes the maths works fine, but it is not based in the real world. It is theory not practice. You can run simulations and derive mathematical connections but there is no living (or dead) proof that they actually happened. And there is a great deal of evidence that the changes you require cannot happen the way you claim them to. Not because of the maths but because of the physiology (and ecology) involved. Nature is not based on mathematics. Then there is the Chaos theory which undermines any sort of mathematical order. And the decay theory that is the reverse of (new) creation and progress. It is almost as if a group of mathematicians shut themselves off from reality and went hunting for patterns and mathematical models without any thought about how these models would be manifested in the real world.
Like I said, DNA did it is no better than God did it. Only God is not scientific. So you are left with clutching at straws and the only vaguely plausible methodology available to you.

Richard

Why do you think complexity is a problem, and how is it anything other than your subjective opinion?

That idea was heavily considered in the 19th century. It lost out to Darwin and Russell’s ideas because those ideas could explain evidence that the designer theories could not. This is still the case.

That’s how it really does work in the real world. People have been exonerated or found guilty in courts based on this math. Investigators have tracked down serial killers using this math:

Why would that have to happen?

The mathematical connections are the proof.

Like what?

What are you talking about?

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I can’t resist throwing this in – it’s both fun and informative, though if you have a player where you can slow it down you’ll catch more detail since so much of it goes by rather swiftly–

It’s worth pausing and taking the various diagrams one step at a time to see what’s going on.

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Obviously theories in science that you are not familiar with.
Chaos theory

The other one is harder to track down becasue decay theory has been hijacked to refer .to memory loss, Basically it is the theory that from the moment of inception everything starts to decay.

Because you cannot just change from one complex system to another. There is no intermediary point which is viable for living. It is literally all or nothing. Lose one element and the whole system collapses. Like taking the spark plug out of a petrol engine (A diesel glow plug will not do it) You can change from a petrol to a diesel but during the process the vehicle is basically dead. And it is not just the engine, you have to change the fuel system, the electrics and so on. Nature cannot be put in suspension while DNA changes the system. Not to mention the incompatibility with the doner (mother) creature for nurturing.

Ecology shows creatures needing other creatures. One cannot develop without the others developing in parallel. Evolution cannot span species or work in parallel.

Richard

Sorry, but I argue FOR Genesis when the topic is the text. What I argue against is uninformed opinion backed up by specious logic and founded on inability (or refusal) to understand. You insist that evolution isn’t true because God, but your position is so lacking in comprehension of the actual evidence that the choice you leave is not a choice, it;s the conclusion that God is a liar.

You know, I’m getting really tired of you making stuff up about people, which is what you’re doing since you plainly haven’t bothered actually following people’s arguments.
The one ignoring complexity is you because you want to throw out the real complexity and pretend it’s just “common building blocks” when you don’t even understand what the actually building blocks are, as was quite evident when you claimed there’s a gene for a leg.

I have yet to see one, and I’d love to find an actual example. Observing my professors in my university days showed me just how wrong your claim is because one thing they all delighted in was finding something that another researcher had overlooked. Glossing over any aspect in a research paper is a good way to look like an idiot – or at least to get treated as one – so great efforts are made to not overlook anything (which is one thing that professors use their grad students for: before publishing a paper, it isn’t at all uncommon for a professor to hand copies to his grad students with the instruction to find anything that so much as appears to be a flaw.

Again, rubbish – or as Martin Luther might say, excrementum.
What actual scientists will not “consider” is that a Designer can be measured or tested for – and that’s true whether the scientist is a Buddhist, a Christian, a Hindu, a Jew, a Muslim, an agnostic, or an atheist. And unless someone proposes a testable hypothesis that could show whether a Designer is/was involved, all honest scientists will continue to operate on that basis.

The problem here is that you don’t understand science at a very basic level.

You claim this, but you never offer an alternative except to stop dong a great deal of science.

LOL

This is a true OMG moment because it shows you have no idea what chaos theory is about – it doesn’t undermine mathematical order, it relies on such order.

No, because “DNA did it” is based on billions of data points that fit together superbly if DNA “did it”, plus it has predictive power and can thus be tested – while “God did it” is a useless hypothesis because there’s no scientific test for it.

There’s nothing “vaguely plausible” about evolution, or for that matter about scientific methodology. It’s evident that you want to think so because that helps fortify your quasi-YEC theolofy and pseudo-science, but what your claiming that really demonstrates, as seen in this thread, that you aren’t interested in buckling down and actually studying the science.

I have had enough. We are going round in circles. I have said my piece(s) let it lie.

Richard

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Chaos theory is about order and how systems follow “law and order”; it tells us that when we used to think that many systems were totally random and thus unpredictable we were wrong.

You’re not talking about science here; there just aren’t any places where things “change from one complex system to another”.

We’re “going round in circles” because you reject actual science and plainly aren’t interested in learning. In terms of the topic, you’re inventing imaginary gaps where there aren’t any – which is a big reason that many people in science reject Christian belief because positions like yours make Christians look like idiots to people who actually do science, and that includes Christians who actually do science.

It makes me think of one of my geology professors along with John Lennox: when that geology professor was asked how he could possibly be a Christian since Christians believe X (which was very similar to the position you’ve been presenting here), my professor asked if the questioner had examined the pertinent data, and when asked what that meant he said that a scholarly examination of the teachings of the Bible will show that such positions are neither required nor presented – or in Lennox’ terms, the questioner isn’t asking about the Christian God.

I am familiar with Chaos theory. What I am asking is how in the world you think it undermines any sort of mathematical order. Have you heard of a Gaussian curve?

You also mention “decay theory”. What are you referring to, and how does it apply to what we are talking about?

Where is the evidence for this claim? Show us the lineage and prove that there is no possible intermediate point.

History shows us that species go extinct all of the time.

Why not?

It would appear that it is not me who cannot understand what is written here.

Richard

Sure is can. Both predator and symbiotic relationships offer new niches and selective pressure, with a change in one species favoring a change in another. No species is an island.

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