Most people understand that our genes are stored in our DNA but what is less commonly understood is how the cell determines which genes to use at any one time. The DNA in our cells contain tens of thousands of protein-coding genes whose proteins serve a great variety of purposes. They serve as railroad tracks, precision tunnels, enzymes to speed up reactions and environmental sensors to name just a few. And some proteins go back to the DNA and bind to the double helix, as part of a complex regulatory network that determines which genes to use to make new proteins. In other words, the cell determines which genes, to use to make new proteins, by using existing proteins. But from where did those existing proteins come?For evolutionists, the question of how DNA regulatory proteins arose is not simple for a number of reasons. One of them is that only a few DNA sequences successfully code for such a protein. Of course the protein structure must fit together with the DNA structure it regulates, and only a small fraction of the possible sequences provide such a structure.
But beyond this, new research is now showing that the protein’s amino acids that make contact with the DNA can be highly restricted. For one particular DNA regulatory protein, the research showed that for the roughly four amino acids that are important in binding with the DNA, only certain amino acids provide acceptable binding. Only about 1 in 50,000 random tries would work.
And that is only for those four amino acids, out of the hundreds comprising the protein. Given the additional structural constraints the odds are much worse. These results are consistent with experiments that show that a DNA binding protein is a 1 in a 1,000,000,000,000 (million million) shot.
And all this only buys a DNA regulatory protein. It is exceedingly unlikely that the protein would bind to the right places along the DNA double helix. It is also exceedingly unlikely that the protein would bind at the right time.
Evolutionists seek to explain the origin of such regulatory proteins, and the greater regulatory network, in terms of gradual pathways. But the above hurdles are not easily avoided and science does not reveal this to be a high probability event. Beyond speculation evolutionists have no explanation for why this is a likely event.
Of course the idea that regulatory proteins and networks evolved does not come from science, it comes from the belief that evolution is true. Strip that away and all that is left is story telling about unlikely events in the name of science. Religion drives science, and it matters.
Regulatory networks require knowledge also- knowledge of what to regulate, when to regul;ate it and how much to regulate it.
ReplyDeleteBlind, undirected molecules do not hold such knowledge.
Cornelius Hunter: These results are consistent with experiments that show that a DNA binding protein is a 1 in a 1,000,000,000,000 (million million) shot.
ReplyDeleteThat means that if you take a few quadrillion random sequences, many will fold into functional proteins. And a quadrillion (10^15) is only a very tiny fraction of a mole (6 * 10^23). From there, these proteins can evolve into a myriad of configurations.
As for your cite to Maerkl & Quake, the entire paper discusses plausible evolutionary pathways saying, "To evolve new transcriptional regulatory network connectivity by slow, gradual drift of TF specificity through single-site mutations therefore is possible, but it also seems to be suboptimal, suggesting that network evolution is probably mainly driven by reshuffling of existing DNA binding domains, evolving new DNA binding sites, gene duplications, or other more plastic regulatory methods, such as posttranscriptional regulation of gene expression."
You may say it is mere speculation, but that is simply not how science works, which is through the testing and proposal of hypotheses. The vast body of evidence strongly supports evolution, including the capability of evolution to devise complex structures. The study restricts certain evolutionary pathways, but supports other plausible pathways.
Cornelius Hunter: Of course the idea that regulatory proteins and networks evolved does not come from science, it comes from the belief that evolution is true.
ReplyDeleteSuch a general statement can't be argued by looking at particulars in isolation, but only by looking at the bulk of the evidence—starting with the evidence for Common Descent.
Cornelius -
ReplyDeleteIn form, this post is rather similar to a couple of other recent ones on your site here - first you outline a biological process/state of affairs. Then you state what you think is evolutions's account of why/how it happens, and then state (rightly or wrongly) why you think this answer is incorrect/insufficient.
I won't pretend that the particulars of these posts don't go over my head a little. But I would like to question your logic in arguing this way. What lesson do you want your readers to draw, exactly?
Because the one thing you never mention which is glaringly conspicuous by its absence is an alternative theory/explaination which WOULD account for the phenomenon you outline.
So, to be blunt, what exactly is your point? Let's just assume for argument's that your posts are entirely correct (a point which I believe remains to be established), so what? If the theory of evolution fails to account for something and no other viable theory accounts for it, then it is a mystery, correct?
Are you merely trying to demonstrate that there are still mysteries in biology: things which we cannot fully account for? Because I don't believe anyone would argue with you on that point.
You often end posts with 'Religion drives science, and it matters.' But that is not something you have established. If you believe the theory of evolution is flawed in its account of a particular phenomenon, then you believe the theory is flawed - a bad theory, maybe, but that does not make it religion! Is it religious to accept a theory which accounts for 95% of the data, even if there still remains an anomalous 5%?
Or perhaps you want your readers to simply make the assumption that other, competing 'theories' are suddenly more credible if evolution is less so?
Or perhaps you have a different reasoning altogether...?
Zachriel:
ReplyDeleteThat means that if you take a few quadrillion random sequences, many will fold into functional proteins. And a quadrillion (10^15) is only a very tiny fraction of a mole (6 * 10^23). From there, these proteins can evolve into a myriad of configurations.
Where did you get the random sequences from?
Zachriel:
The vast body of evidence strongly supports evolution, including the capability of evolution to devise complex structures.
Again with the mindless equivocation.
Evolution isn't being debated and blind, undirected processes have never been shown to have any capability beyond breaking things.
Zachriel:
ReplyDeleteSuch a general statement can't be argued by looking at particulars in isolation, but only by looking at the bulk of the evidence—starting with the evidence for Common Descent.
The same evidence that can be used to support Common Design and/ or convergence?
The same evidence that excludes the mechanisms?
IOW what "evidence" are you talking about?
Ritchie,
ReplyDeleteOne does need to produce an alternative to show that the current "theory" is BS.
Joe G: Again with the mindless equivocation.
ReplyDeleteThe comment refers to changes in heritable characteristics in populations. This was already clarified for you previously.
Joe G: Where did you get the random sequences from?
That is irrelevant to Cornelius Hunter's original claim.
Joe G -
ReplyDelete"One does need to produce an alternative to show that the current "theory" is BS."
BS? But he is not showing us that.
There is a vast deal of evidence that the theory of evolution accounts for. Cornelius is focussing his posts here on very specific biological phenomenon which either he misunderstands or the theory of evolution is at a loss to account for (I really don't think I'm qualified to judge which).
Either way, that does not detract from the vast deal of data the theory of evolution DOES account for.
So even if he is correct in his posts (big if), then the phenomenon he discribes will at best be mysteries to be further examined. Not positive evidence for any hypothesis which cares to contradict evolution.
Zachriel:
ReplyDeleteThe comment refers to changes in heritable characteristics in populations. This was already clarified for you previously.
IOW equivocation. Your "evolution" is not being debated.
So why even use it?
I say it is to be deception.
And you are deceptive because that is all you have.
Also the origin of those random sequences is very relevant as the debate is all about origins.
IOW if living organisms arose from non-living matter via blind, undirected processes then the points being made on this blog are moot.
Ritchie,
ReplyDeleteWhat is this alleged vast deal of evidence the theory accounts for?
What is the testable hypothesis for blind, undirected processes?
And as I said before the positive evidence comes from regulatory networks which require knowledge in order to properly regulate.
Blind molecules do not have that knowledge. Programmed molecules would.
Is that easy enough for you to understand?
We're dealing with some of these points in our movie Watchmaker, soon to be a major motion picture. Yes, I made this post about me :)
ReplyDeleteThe bigger issue is, evolution is still a theory, that hasn't been absolutely proven. Despite what the "Science is settled" crowd would have you believe.
Ask yourself, what's more likely, that we came from a rock, or that there was some ID going on? The simpler solution is actually creation.
PS, true randomness doesn't exist. Just ask any mathematician.
I do not understand why there is a conflict between intelligent design and evolution. Do people forget that we are a result of evolution and we consider ourselves intellegent. Are we to beleive that we are the first intellegent species in evolution, or is evolution itself intellegent. All that "junk" dna may be the next step in our evolution being written by intellegent DNA, the first intellengent life form. Human are so vain in beleiving they are the only ones that can create.
ReplyDeletePeople hate intellegent design because when they hear god they assume something outside of them selves created them. We should think of intellegent design as something biology, evolution and DNA designed.
Joe G -
ReplyDelete"What is this alleged vast deal of evidence the theory accounts for?"
I've given you a more detailed list in the thread two posts ago (about ribosomes). If there's any one field you want to discuss in greater detail, I'll be happy to. Suffice to say the evidence stretches across many fields of biology.
But let me take a single case just as an example. I've just finished reading a book by the man who discovered the Tiktaalik (called Your Inner Fish, I highly recommend it). It is a serious contender for our fish ancestor who came up on land.
Tiktaalik was discovered in 2004. I dislike thinking in terms of 'missing links' simply because the term is so mis-used and misleading. However, if we wanted before 2004 to get as close as we could to the fish fish to come onto land, the best we could do would be amphibian-like fish (such as Eusthenopteron and Panderichthys), or fish-like amphibians (such as Ichthyostega).
Th fact that these creatures were so anatomically similar was telling. As was the timing; we find such creatures as Panderichthys at about 380 million years ago, and our earliest discovered amphibians date from around 365 million years ago.
Then Tiktaalik was discovered. Dated at around 375 million years ago, it almost perfectly splits the difference between fish like Panderichthys and amphibians like Ichthyostega.
"Like a fish, it has scales in its back and fins with fin webbing. But ,like early land-living animals, it has a flat head and a neck. And, when we look inside the fin, we see bones that correspond to the upper arm, the forearm, even parts of the wrist. There are joints there, too: this is a fish with shoulder, elbow, and wrist joints. " (p23) It was the first fish 'that could do a push-up'!
Now is the discovery of this fish not a great vindication of the theory of evolution? It naturally claims that fish such and Panderichthys are the ancestors of amphibians like Ichthyostega. And then there came a 'missing link' - a creature which was not only exactly halfway between fish and amphibians, but found at the right time!
How does Intelligent Design account for this discovery? Are we to believe that fish such as Tiktaalik just happened to live after Panderichthys and before Ichthyostega, and yet was unrelated to either, despite the obvious anatomical similarities?
"Blind molecules do not have that knowledge. Programmed molecules would."
Molecules have knowledge?
Batman -
ReplyDelete"The bigger issue is, evolution is still a theory, that hasn't been absolutely proven. Despite what the "Science is settled" crowd would have you believe."
Nothing in science is ever absolutely proved. Proof is for mathematics and alcohol. Such a statement simply demonstrates you don't know how science works.
"Ask yourself, what's more likely, that we came from a rock, or that there was some ID going on? The simpler solution is actually creation."
Who is arguing we came from a rock?
Biologists are simply arguing that the first, most basic biological bodies came from chemical ones.
Creation is not the simpler explanation, because it necessitates a creator - a being who is more improbable than almost any other imaginable thing. I really don't know what could be LESS likely.
Batman:
ReplyDelete"The bigger issue is, evolution is still a theory, that hasn't been absolutely proven. Despite what the "Science is settled" crowd would have you believe."
Well evolutionists agree that the question of how evolution occurred is very much merely a theory, open for revision and correction. But that evolution, one way or another, occurred is an undeniable fact.
The bigger issue here is not that evolution is "just a theory, regardless of the claims of evolutionists." If this was an argument about scientific evidence evolution would have been dropped a long time ago.
Evolutionists have not make scientific mistakes. They never claimed to know just how, in all the details, evolution occurred in the first place.
This is not about science, it is about metaphysics.
Ritchie,
ReplyDeleteI read that book last year.
Recent findings say that all Shubin et al., found was a mosaic that lived in ancient environment similar to that of mosaics today- mud-skippers,etc.
IOW the recent findings say that Tiktaalik came after the transition was already made.
And yes biological molecules- in the design scenario- would have knowledge in the same sense spell-check has knowledge.
They would also have knowledge in the same sense data packets know where to go in a communication network.
Cornelius -
ReplyDelete"This is not about science, it is about metaphysics."
I really think this is the cause of your confusion.
Allow me to draw for you a distinction between methodological naturalism and metaphysical naturalism.
Methodological naturalism is the belief that the universe is governed by natural laws that we can study and understand. There are no supernatural interventions in the way the world operates. This is what science employs.
Metaphysical naturalism is the belief that no supernatural exists AT ALL outside of these natural laws. Science does NOT require this belief.
Science does not insist that the supernatural exists or that it does not. Such a matter is simply beyond the realms of science. However, it DOES insist that we assume all events we can observe and study are natural in origin. This is a totally necessary prerequiste in performing science.
Perhaps I myself have not made this point clear enough. If so, I apologise. Science does not insist that the supernatural does not exist, but it does necessitate not posing it as an explanation for any observed phenomenon. This is merely a stipulation necessary to performing science at all.
I believe you are simply confusing methodological naturalism and metaphysical naturalism, and THIS is the cause of your complaint. If so, I could well understand why. But science does not insist on metaphysical naturalism. If it did, it would insist that its practitioners were all atheists.
The fact that there are religious scientists should tell you this is wrong.
Now, you keep saying 'religion drives science'. This would only be true if science insisted on metaphysical naturalism. It doesn't. It only insists on methodological naturalism. You can be a scientist and believe in whatever deity you like - as long as you do not start posing miracles as explanations in your scientific work.
But you apparently desire the ability to pose a miracle as a credible scientific explanation? What can be your motive, I wonder. Perhaps a conviction that miracles actually HAPPEN (despite the fact that there is absolutely no evidence for this)...?
But then, that would be an opinion driven by religion, wouldn't it?
Joe G -
ReplyDelete"Recent findings say that all Shubin et al., found was a mosaic that lived in ancient environment similar to that of mosaics today- mud-skippers,etc."
Ummm, who says that, exactly?
"IOW the recent findings say that Tiktaalik came after the transition was already made."
I assume you mean the tetrapod footprints discovered this month in Poland which pre-date Tiktaalik by 10 million years?
Well that's a fair point. And this is one of the reasons I don't like the term 'missing link'.
Let me be clear, Neither I nor the theory of evoloution in general claims that Tiktaalik itself definitely WAS the first fish to walk on land, and nor that it was the DIRECT descendant of Panderichthys nor the direct ancestor of Ichthyostega (or, much later, us).
Take archaeopteryx, for example. No-one is claiming that is was THE direct descdant of all birds (in fact I believe we now know it was not). But what it does show is that at this time, in this part of the world, bird-like reptiles were developing from dinosaurs.
The same with Tiktaalik. It is probably a representative of a group of amphibian-fish. Possibly very closely related to the first fish to walk on land, but probably unlikely to be THE species itself.
What it shows is that amphibian-like fish were developing and coming onto land, with their necks and their shoulders, and their arm bones at the right time.
Tiktaalik is unlikely to be THE very first species of land-walking fish, or indeed our direct ancestor, but it is more than likely extremely closely related. Perhaps, for example, as closely related as a huskie is to a wolf.
"And yes biological molecules- in the design scenario- would have knowledge in the same sense spell-check has knowledge."
But the design scenario would also account for the molecules NOT having knowledge. Is there really any possible, hypothetical evidence at all that the design scenario could NOT account for? Any evidence that could possibly falsify the design theory? Surely if your theory rests on shrugging your shoulders and saying 'A great, divine, cosmic designer made it like that', then such an explanation couyld be applied to any POSSIBLE piece of evidence?
Ritchie:
ReplyDelete"I really think this is the cause of your confusion. ... Science does not insist that the supernatural exists or that it does not."
But then again I never said otherwise. Unfortunately this is typical. I'm unable to respond fully to your comment simply because it would take too long as it is packed with misreads.
I suppose it would be cheeky to ask you to explain your position more clearly in it's own post...?
ReplyDeleteBecause if you agree that science does not insist on the existence or non-existence of the supernatural, then I fail to see why you insist it takes a metaphysically theological stance at all.
Surely it would only do so if it insisted on metaphysical naturalism, not merely on methodological naturalism?
Why does every step in evolution have to be random. Why can't it be planned. Not every plan works there for it is still random as to what survives and what doesn't. In there no middle ground in this argument?
ReplyDeleteRitchie,
ReplyDelete1- Evidence for Common Descent is not evidence for a mechanism- this debate is all about mechanisms. Are all mutations genetic accidents or are they the result of built-in responses to environmental cues?
IOW were organisms designed to evolve?
As for Tiktaalik- as far as you know it wasn't transitioning into anything. That is the way it was, always was and died out that way.
As far as birds are concerned that transition also only exists in imagination-land.
So if imagination is now considered scientific evidence your Common Descent has plenty of it.
As for the design inference it is all about reduction and requirements.
Once the requirement for a designer is gone so is the design inference.
Ya see the explanatory filter mandates that we consider chance and necessity first. And after that some specification must be met.
So if someone says that is designed because of X and Y all you have to do is show that one of those doesn't apply.
Joe G -
ReplyDelete"IOW were organisms designed to evolve?"
I know I'm not very up on the scientific details here, but isn't this begging the question here that organisms were 'designed' at all?
"As for Tiktaalik- as far as you know it wasn't transitioning into anything."
True. I can't show with 100% certainty that creatures such as Titkaalik descended from other such as Panderichthys and into creatures such as Ichthyostega. But the theory of evolution would predict such a creature and its discovery is a vindication of this prediction.
Do you really find it intellectually satisfying to imagine that this creature JUST HAPPENS to have appeared on Earth just after ambibian-like fish and just before fish-like amphibians, and sporting features midway between each and yet totally unrelated to either? That's a pretty massive co-incidence, don't you think? The chances of it happening have to be phenomenal.
"As far as birds are concerned that transition also only exists in imagination-land."
Errr, no it doesn't. We have plenty of fossil evidence of dinosaurs developing important bird-like features (such as feathers).
http://en.wikipedia.org/wiki/Feathered_dinosaurs
"As for the design inference it is all about reduction and requirements.
Once the requirement for a designer is gone so is the design inference."
So basically your design inference is based on God of the Gaps train of logic? As long as their are biological mysteries, there is always a gap in our knowledge in which evidence for your longed-for 'designer' MIGHT hide, and thus the design inference is still possible?
Or are you even going as far as to propose that the design inference should be the default 'theory' we accept - that we should consider it true until we can prove otherwise? I'm afraid science doesn't work like that.
Ritchie,
ReplyDeleteYou don't go looking for transitionals AFTER the transition occurred.
Also there isn;t any genetic evoidence to support the alleged transformation from fish to tetrapod.
There isn't any genetic data to support the transformations required to go from dino to bird.
There isn't any way to objectively test either premise.
And there sure as heck isn't any way to test if they evolved via an accumulation of genetic accidents.
As for "God of the gaps" I am not religious.
Also the design inference is based on our KNOWLEDGE of cause and effect.
As for default- you are not reading what I post.
The EF MANDATES the all other causations be considered first.
And yes as with ALL scientific inferences the design inference can either be confirmed or refuted by future research.
All that said all you have to do is to actuall support your position and ID would fade away.
But you cannot so you argue against ID without even undersdtanding what it is.
I assume someone has already done the math but how far can a single mutation go in a population of over 6 billion?
ReplyDeleteJoe G
ReplyDelete"You don't go looking for transitionals AFTER the transition occurred."
As I said, it was always highly unlikely that Tiktaalik was THE very first fish to walk on land. But it is probably extremely closely related. It is just too perfect a match in every respect. But are you committing yourself to the idea that this is just a coincidence? Do you really appreacite the odds of just such a perfectly seemingly intermediate creature just happeneing to 'appear' at just the right time?
"Also there isn;t any genetic evoidence to support the alleged transformation from fish to tetrapod."
Do you mean apart from comparing the skeletons of, say, Panderichthys, Tiktaalik and Ichthyostega side by side and noting the remarkable similarities?
"There isn't any genetic data to support the transformations required to go from dino to bird."
Wrong. There are fossils which demonstrate dinosaurs with avian features, such as feathers. In other words, we have evidence a small family of dinosaurs developing bird features. That's pretty good evidence. Given this, why do you oppose the idea that the dinosaurs became actual birds?
Besides which there is also this:
http://www.timesonline.co.uk/tol/news/environment/article3811158.ece
And this:
http://www.guardian.co.uk/science/2009/sep/24/dinosaur-fossil-discovery-china
"As for "God of the gaps" I am not religious."
I was referring merely to the logic your argument seems to be governed by. "As for the design inference it is all about reduction and requirements. Once the requirement for a designer is gone so is the design inference." To me this sounds rather like 'To prove ID wrong, evolution just has to solve every single biological mystery, leaving no place for evidence of ID to potentially hide'. Your do not have positive evidence for ID, you are merely pointing to biological mysteries and claiming evidence for it COULD lie in there. But if and when there mysteries are conclusively solved, you will simply retreat back to the next mystery and insist your evidence lies in there...
"Also the design inference is based on our KNOWLEDGE of cause and effect."
Elaborate please.
"The EF MANDATES the all other causations be considered first."
What's the EF?
"And yes as with ALL scientific inferences the design inference can either be confirmed or refuted by future research."
So you keep claiming. But you don't actually state what possible evidence could possibly falsify it.
binbots -
ReplyDelete"I assume someone has already done the math but how far can a single mutation go in a population of over 6 billion?"
I'm not sure I understand the question. What do you mean, please?
A single mutation will be confined to the one individual who has the mutation, surely...?
I mean how far over time, with successful breeding, will the (better) mutation go/spread.
ReplyDeleteWell, potentially to the whole population.
ReplyDeleteAssuming there is gene flow between all members of the population.