Probably in response to Nick Matzke here and here, proposing among other things an onion test. A friend of UD News writes to say,
Those who employ “the onion test” should recall that the test — as originally formulated by geneticist T. Ryan Gregory — asks for a “universal function” for non-coding DNA. Is this a biologically reasonable question to ask? No. As Jonathan Wells writes, in The Myth of Junk DNA (pp. 85-86):
The “onion test,” according to Gregory, “is a simply reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?” [1]
Gregory directs his challenge to “anyone who thinks they have come up with a universal function for non-coding DNA.” Yet there probably is no such person. As we have seen, scientists know of many functions for non-protein-coding DNA. Nobody claims that there is “a universal function” that applies both to mammals and to onions. Based on the evidence, scientists have proposed that non-protein-coding intronic DNA helps to regulate alternative splicing in brain cells, and that non-protein-coding repetitive DNA plays a role in placental development. Why should those scientists justify their proposals by referring to onions, which have neither brains nor placentas?
See also: Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”
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Interesting. When the facts start getting inconvenient, bring out the lawyerly hair-splitting.
Unfortunately the facts are still inconvenient for you. Most of the difference in genome sizes is typically due to repetitive elements. Gene counts etc. don’t change very much even between genomes with hugely different sizes. If you’re going to claim, as ID advocates have again and again and again, that junk DNA is a crock, scientists were idiots for ever believing in such a thing, and most/all DNA is functional, you need to explain why some onions need multiple human genome’s worth of DNA more than other onions, and why onions in general have genomes many times the size of the human genome.
Otherwise, the argument that a lot of the DNA in organisms with large genome isn’t doing much is pretty strong. After all, you can build an onion with a few human genomes worth of DNA, so clearly building an onion with 20 human genomes worth of DNA is not strictly necessary.
This is a interesting comment from Gregory, the originator of the onion test, at the bottom of the page:
Are you listening Nick???
Nick,
Your statements are deeply rooted in assumptions. Maybe they are accurate assumptions. But why not question them?
You assume that there are only two possibilities. Either the onion needs the extra DNA to function, or it is junk. That assumption naturally follows from other assumptions. Maybe you’re right on both counts. But it’s odd that in a field dependent on boundless imagination that’s all you can come up with.
Shouldn´t darwinist explain first how one onion specie has 7 times the genome size of other onion specie from a common ancestor via RM + NS?
Whole genome duplications are common in plants, and have occurred in animals.
http://en.wikipedia.org/wiki/Polyploid
Perhaps a little thinking outside of the ‘central dogma’ box?
Notes:
Also of interest in the following paper other than the quote that is excerpted, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis) model of neo-Darwinism.
Eugene Koonin also agrees that the modern evolutionary synthesis (Genetic Reductionism/Central dogma) is devastated.
Dr. Sternberg has also come out very hard against ‘neo-Darwinian narratives’;
Further notes:
verse and music:
Blas, as with Petrushka’s cite, all you are ever going to get from neo-Darwinists is misdirection that never addresses core questions such as what is the functionality for why the genome size is at it is.
I myself noted this on the other thread:
http://www.uncommondescent.com.....ent-402596
Then why in blue blazes are you using the word ‘junk DNA’ to further your atheistic philosophy, instead of using “non-coding DNA” so Gregory suggests. But then again it is not about the science is it Nick??? It is about your religion!!!
Petrushka, let’s assume for a moment this is correct. What does it tell us about junk DNA generally? Not much. No-one disputes that duplications occur.
This issue is that the iconic myth of “junk DNA” in humans has been shouted from the rooftops, over and over and over again, as a wonderful example of bad design and a confirmation of Darwinian evolution. That assessment has turned out to be spectacularly wrong, which, according to the Darwinists’ own logic then, must operate as a *refutation* of the Darwinian mechanism. You can’t have it both ways. Either junk DNA is irrelevant and never did support Darwinism in the first place, or it is relevant and has refuted Darwinism in the case of human junk DNA.
Now the Darwinist lobby moves on to another example of what they think is junk DNA, in Nick’s case, apparently misrepresenting what Gregory intended to say and making pronouncements without having the faintest idea whether the DNA is junk or not.
The real kicker is that ID proponents don’t dispute that machines break down, that code can get messed up, that errors can occur in the history of life. In contrast, the materialist cannot accept even a single example of design in the history of life, or his whole materialistic enterprise goes up in smoke. Some of us are willing to look at the world, realize some things are designed and others aren’t, and then delve into the interesting question of whether and how we can detect which things are designed. The materialist can never even grasp this interesting question, because it lies beyond his philosophical blinders.
This is true, but I believe the onion genome sizes are all haploid values, i.e. it is not a matter of diploids vs. tetraploids vs. hexaploids etc.
The usual explanation for dramatic differences in genome size is self-replication of the repetitive elements. LINES, SINES, etc. can easily get copied again and again in the genome, blowing up its size.
Genome size is determined by a balance between genome-growing elements such as LINES and SINES, and removal mechanisms like deletion. The only interesting question is whether or not some higher-level factor like selection favors particular genome sizes, and thus spreads insertions in some genomes, and deletions in others, or whether genome size is just a byproduct of e.g. population size, where extra DNA is always deleterious, but very mildly so, such that only in very large populations with rapid generation time is selection strong enough to favor the very weakly beneficial deletions.
I am just opposing the numerous statements of the ID movement to the effect that junk DNA was a stupid idea, that the genome is “chock-full” of digital code, and that most/all of the genome is functional. Gregory is making a narrow point about the confusing history of the term. He certainly does not, though, think it is valid to declare or assume that most/all of the genome has organismal function, especially some kind of sexy, informational function, which is what IDists usually imply.
When I use the word “junk”, I am referring to the “no very important function” position. The primary, and very, very, good, evidence for this position, is that it is manifestly true that some organisms have way more DNA than is really required to build them, and we know this for a fact because basically similar organisms (even the same genus, or sister species) have much, much less DNA.
And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side.
as to this comment:
Nick that is far from the ONLY question, and in my view is secondary to the question of what epigenetic mechanism is driving the variance. For you to presuppose the variance is completely random is to completely ignore where the cutting edge science is at right now (Shapiro for one cite), And indeed I would hold you position to be a science stopper!
Now who is being the lawyer Nick???
Here’s the answer to the onion test:
Namely, that not all introns are functional. Many introns are functionless. Nevertheless, under a teleological perspective, the first introns were functional. Not all introns are functional because of whole-genome duplications. Let’s say we have an onion with a small genome size. That genome is duplicated. There is no selective pressure to preserve the function of the duplicated introns (just like duplicated genes can often tolerate far more mutations than the original gene), and so the duplicated introns become functionless. Repeat this process several times and you have an onion population with a large genome size and large chunks of functionless introns. Nevertheless, the first introns were functional. This answers the onion test from a teleological context.
Nick,
You’ve just finished calling it junk. Maybe you’re right. But why would selection favor either junk or specific genome sizes? If that were the case, then by definition the extra genes would be advantageous, therefore functional. This is true even if you overlook the circular logic that cannot distinguish between advantage and selection.
Are you redefining natural selection so that it can “select” was does not affect differential reproduction? Or are you admitting that it’s a tautology, defined as whatever survives, including enlarged genomes? Or are you saying that the enlarged genomes actually do provide a selectable advantage, contradicting everything you’ve just said before?
Nick this is OT, but in case your interested, Holly Ordway, a former atheist, is interviewed by Apologetics315 here;
http://www.youtube.com/watch?v=uA4pho7QfVw
You can’t just toss around the word “epigenetics” like it means whatever poorly-specified notion is in your head. Saying that epigenetics determines genome size is a contradiction in terms — epigenetics is what happens on top of the genome, e.g. methylation. If the genome size changes, that’s genetics, straight-up.
You haven’t been reading what I’ve written, I’ve already laid out the two major ideas in the scientific community, see here:
http://www.uncommondescent.com.....ent-402595
and here:
http://www.uncommondescent.com.....ent-402687
That’s right! Quit tossing around words starting with “e” that mean just about anything and everything! (Except “everything.”)
For this stuff to make any sense to you, you would have to understand the influence of population size on selection/drift balance, I don’t have time to explain it, maybe someone else will.
Nick,
I did read it. You can’t have it both ways. It’s junk. It has no function. It does have a function, but one that doesn’t technically count as a function.
The more you carry on about what you think you might know about genes, their purpose or lack of it, the more it underscores that most of of it over your head. I don’t mean that as bad as it sounds, because you clearly know a great deal.
I know what it sounds when someone tries to sound even smarter by stating what they don’t know. It sounds like this:
Notice how you admit to not knowing why there is a difference in genome size (no problem there) but then lay it on pretty thick as you suggest that you’ve got it narrowed down to two distinct possibilities while leaving the door open for other unnamed ‘higher-level factors.’
Most people only need a few words to say they have no idea, and then I trust them more when they say they do know something. I had a friend who talked like you. I can hear it a mile away.
Well Nick, perhaps we should just go a little deeper into exactly what kind of epigenetic information we are dealing with;
A few comments as to ‘non-local’ epigenetic information:
Though when many people speak of epigenetic information they are mainly focused on information flow in the cell that is not DNA centric in its basis, such as the many examples of epigenetic information flow Dr. Shapiro lists on page 22 of this following paper: ,,,
,,,There is a particular type of extra ‘epigenetic’ information in life, that is not listed in Dr. Shapiro’s paper, that is very important for people to consider. To give a little background on this ‘extra’ epigenetic information, Dr. Stephen Meyer comments at the end of this following video,,,
So exactly where does this mysterious information, that Dr. Meyer illustrates the necessity of, that controls the overall ‘biological form’ of a organism, actually reside if not in DNA coding??? I think a very strong case can be made that it is ‘non-local’, beyond space and time, quantum information, which is not reducible to a material basis (A. Aspect), that is what is actually in control of, and orchestrating, the biological forms of organisms to be in the particular ‘3D shapes’ we find them in.,,, To show the plausibility of this, first we find that DNA itself would not even have its necessary helical shape/structure if it were not for ‘non-local’ quantum information/entanglement holding it in that particular shape;
As well, DNA is shown to do ‘chemically impossible’ things here, thus, once again, demonstrating ‘non-local’ information’s overarching control of ‘3-D form’ in molecular structures:
As well, At the 6:05 minute mark, of this following video, cells are witnessed as they pull themselves together, from a distance, to form ‘flawless’ blood vessels. The commentator on the video refers to the ‘at a distance’ action of the cells as a ‘miracle’;
Next we also find that non-local, beyond space and time, quantum information/entanglement is also necessary for dictating the final shape that proteins will take upon protein folding;
Another very interesting piece of evidence, that ‘non-local’ quantum information/entanglement is dictating the shape of a organism, comes forth when we realize that the ‘4-Dimensional shape’ of a organism fairly quickly disintegrates to 3-dimensional thermodynamic equilibrium upon the death of the organism:
As well it is very interesting to note that this quantum information/entanglement, which will assuredly be ‘totally missing’ from the organism, once the organism disintegrates to complete thermodynamic equilibrium, is shown to be ‘conserved’. i.e. This transcendent non-local quantum information, though missing from the dead, and now disintegrated, organism must reside somewhere ‘in the universe’:
It is clear that a very strong case is now evident, that ‘non-local’ quantum information/entanglement is in fact the ‘highest level’ of epigentic information in organisms, and that it is this non-local, beyond space and time, epigentic information that is, in fact, ‘shaping’ 4 dimensional creatures in this 3-Dimensional world!!!
Music:
Got it, Nick, the genome sizes of onions are an effect of their population size. That would explain why raspberries have a genome about 8% the size of ours. Or does it? And that would explain the difference in genome sizes within onions of the same population. Or does it?
If you ever have time to explain it to me, don’t. Use it to describe to me the incremental genetic steps, both the variation and selection, leading from a glue trap to a flypaper trap. Sadly you’ve used up all your precious time telling me what you don’t know about onions and once again you have none left to illustrate how the cornerstone of biology works.
Come up with that and with your newfound credibility I’ll just take your word for all the rest.
Better audio to music video:
Nick, if Mr Andrews hasn’t worn you out, I could always use another refresher course on the rise of information.
Dude, you are just being angry, not making any sense. Raspberries could well have a larger historical population size than humans. You also have to factor in generation time, growth rate, number of offspring per generation, etc. It seems that fast-growing, fast-reproducing critters tend to have smaller genomes. And it’s just a hypothesis in any case. Might be wrong, but it’s dang well better than “Let’s just brazenly assume everything is functional, despite all the evidence against this idea, and let’s call all the scientists who are aware of the evidence idiots while we’re at it.”
The onions with different genome sizes are not in the same population, they are different species. Take a deep breath and think before you write, dude!
Re: carnivorous plants, “information”, etc. — start a new post if you want to talk about off-topic stuff, there is no point to discussing a million things at once. And, it would be nice if you quoted my previous remarks on those topics and explained why they are wrong, rather than just inviting me to rehash the same basic case I’ve made several times already.
Wow, trying to convert me? And here I thought this ID stuff was just about science, not apologetics.
Listening to this while running a program — she started out being an English Ph.D. by hating Christians, then found out her nice fencing coach was one. This doesn’t really speak to me, as I don’t hate Christians.
I was raised religious but am not particularly now, although I’m not anti-religious either. But, would you like know the biggest thing than made me agnostic about religion? Creationists and their continual, unabated, shameless, eternally uncorrected shenanigans. Once you’ve seen creationists distort scientific evidence, distort the views of scientists, etc., once you’ve seen them refuse to correct such mistakes in themselves and others, once you’ve seen them do this on an industrial and institutional scale, all the while insulting hardworking scientists and blaming them for pretty much every bad thing that has ever happened, it’s hard to not be more than little skeptical of their critical thinking abilities, intellectual honesty (not in the sense of lying, but in the sense of doing “due diligence” before opening one’s big fat mouth about some technical topic), and the rest.
If creationists/IDists want to evangelize people like me, they should start correcting each other’s mistakes before I do, they should start criticizing widespread but indefensible creationist views (like young-earthism), and they should start making arguments that are not shot down by a few minutes on Wikipedia and Google Scholar.
Sorry, Nick. It’s just that you’re so busy and I thought I’d catch you while you have time. Somehow the time always flies away talking about onions and there’s never time to address the central question of how you can know that incremental genetic variations are selected to produce significant diversity in living things when you have not determined or even bothered to imagine a detailed pathway. You know, that one critical piece of information that either validates the theory or leaves it blowing in the wind.
Do you really need me to cite you saying that glue traps evolved into snap-traps by a series of incremental, selected variations? If you don’t think you said that, just tell me.
This is your central dogma, and one of the primary reasons why critical thinkers ridicule darwinism. Having asserted it, why would you ever think the demands for evidence would stop unless you produced it, yielded, or just gave up and went away?
Perhaps someone should start a Please Be Nice to Me I Only Came To Ridicule You But I Get Sad When You Ask Difficult Questions thread. Perhaps the simple question won’t haunt you there.
Nick, It might interest you to know that I find you to be one of the most religious, intellectually dishonest, atheistic neo-Darwinists I’ve ever met!!! And I’ve met my fair share!!! In fact it is such shamelessly intellectually dishonesty on the part of religious atheists such as yourself who have made my faith in the truthfulness of the claims of Christianity that much stronger!!! Before I met people like you I pretty much thought everyone was basically fair minded. But I’ve certainly learnd differently! And for that I thank you, even though I certainly fear for the fate of your soul for trying to lead people away from the truth of God with such shameless, and persistent, deception!!!
notes:
It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as an observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video which was made by two Australian University Physics Professors with a supercomputer.)
Here is the interactive website, with link to the relativistic math at the bottom of the page, related to the preceding video;
Here are some ‘typical’ Near Death Experiences from Judeo-Christian cultures
further note:
Onions have lotsa DNA, therefore, all of biology of have been one massive fluke. The evidence is overwhelming…
LOL — then you ought to be able to find plenty of times where I’ve argued for atheism. I bet you can’t find *any*. It’s not something I do — I am actually pretty profoundly disinterested in theism vs. atheism. I doubt it’s resolvable on objective evidence.
Evolution, on the other hand, is confirmed by evidence almost every place you look, if you take a fair and through look at the primary evidence, and don’t rely on misinterpretations of news stories, wishful thinking based on superficial study, etc. People messing with science, in the teeth of the facts, is what bothers me.
Nick Matzke you deliver priceless commenting gold to have on display here. Please do not stop schooling us ID/creasionist.
So, you really think that it’s unlikely that evolution can quantitatively increase or decrease the amount of mucilage secreted by a leaf? That’s where we left the discussion on the last CP thread.
Why should anyone believe this is unlikely? It’s a simple change in degree, and typically such changes are just a matter of upregulating or downregulating a pathway, which is just a matter of altering the binding strength of a promoter or some such.
Nick: “And atheist philosophy? Puh-lease. The Gnu Atheists bash me worse than you guys for not being on their side.”
Nick, this is good to know, and thank you for clarifying your position. At least you’re in good company!
“Evolution, on the other hand, is confirmed by evidence almost every place you look . . .”
This statement, however, is possible only by the rhetorical trick of conflating wildly different meanings of “evolution,” from the obvious and well-supported to the outrageous and wildly-speculative. Once a person escapes from the intellectual trap of thinking that “evolution” is a single process that operates across the whole of reality, the evidence for “evolution” looks a whole lot more modest.
Nick you state:
Really Nick??? REALLY??? Does this include ‘confirmation’ for THE PRIMARY, and most important, claim of neo-Darwinism that purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present??? Seems to me your grand claims for such irrefutable proof for neo-Darwinism, from the ‘primary evidence’, were just recently shown to be non-existent!!!:
Nick, how quickly you seem to forget this so as to move on the ever important onion argument? 🙂 That episode with Casey Luskin is fairly embarrassing in itself as to shooting down your very own credibility for any claims you might make in the future (a boy crying wolf if you will),,,, yet you also stated this;
Really Nick??? REALLY??? I actually have such anger towards neo-Darwinian atheists for ‘messing with science’! Moreover, It might interest you to know that, ‘science’ would not even be possible if neo-Darwinism were true! Thus if you truly loved science, as you claim you do, then you would in fact be angry with atheistic neo-Darwinists for perverting it so severely to their own personal agenda:
This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.
Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:
further notes:
As well Nick, it might interest you to know, (Actually it will probably be severely ‘inconvenient’ for you to know, since you fight so hard against the truth), that proof for non-locality, (beyond space and time causation), of ‘material’ reality was recently extended past the ‘spooky action at a distance’ effects of quantum entanglement (A. Aspect), to the ‘material’ particles themselves! i.e. Now, a transcendent ‘non-local’ (beyond space and time) cause must be supplied to explain the existence of ‘material’ particles in this universe in the first place:
Further notes:
The following describes how quantum entanglement is related to functional information:
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian worldview of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!
Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!!
verse and music:
Nick matzke:
Nice equivocation, Nick. It’s as if you really believe your ignoirance is some sort of refutation.
ID is not anti-evolution, Nick, so when you say:
What “evolution” are you talking about? Are you talking about:
A) Front-loaded evolution
B) Intelligent Design evolution
C) Blind Watchmaker evolution
Then you should have no problem going into a lab and conducting experiments to demonstrate your claim. In the absence of that you don’t have any science.
Nick,
I thought we were talking about the evolution of a snap-trap from a glue trap. Why are you retreating to a variation in mucilage?
It is both possible and likely. It’s also possible and likely that a variation might result in a rodent having longer forelimbs. That does not explain bats.
When pressed to explain your extrapolation you retreat defensively to a safer position. That’s fine. If you want to say that evolution can increase or decrease the amount of mucilage on a leaf, so be it. We can leave it there and now we both agree on what type of changes evolution can produce.
Nick Matzke:
If the genome size changes due to factors beyond itself and the organism it occupies, then that’s epigenetics, straight-up.
Or, as Dr Spetner put it in “Not By Chance”- “built-in responses to environmental cues”.
Hmm, I guess you didn’t read my previous posts on the other threads after all.
If you agree that evolution can do things like change mucilage secretion levels, then the argument about the origin of the snap trap is over, because I (well, the sources I cited) explained the origin of the snap trap *from* a glue trap with quantitative changes like changes in levels of mucilage secretion.
Pretty please, go back and read that stuff, we had several threads on it, I can’t sit around typing out the origin of the Venus Flytrap over and over and over again.
We’ve had, like, a million threads on the origin of new genes. They typically go like this: someone says “evolution can’t explain how ‘purely material neo-Darwinian processes can, all by themselves without any help from a Intelligent mind, generate functional information above and beyond what was already present’! I explain how gene duplication + mutation + selection can generate new genes with new functions, which is new information on any reasonable definition of “information”. I also give lots of references. Pretty soon the IDists beat a hasty retreat to the origin of life and forget that their original claim was that evolution couldn’t produce ANY new information.
Re: Luskin — his argument is so poor he couldn’t even convince a longtime Telic Thoughts blogger. See guts’s reply, and my reply, here, since Luskin bravely closed the DI thread:
http://telicthoughts.com/casey-luskin-vs-kimura/
My reply to Luskin, which I’ll quote here
http://telicthoughts.com/casey.....ent-277428
Nick,
If you had explained it in previous threads we wouldn’t be talking about it again.
No. They. Did. Not. If the explanation is series of genetic changes which were selected, then it must actually include a pathway of specific genetic changes and describe how or why they were selected.
At best you offer a handful of genetic differences and hope that we’ll give you credit for pointing out the obvious – that two different plants are bound to have identifiable genetic differences.
You insist that such processes effect the change, but then you are unable to explain the changes in the very terms of those processes. You revert to more vague descriptions of phenotypic change.
I’m actually paying attention, so you can’t fake it by telling me that you already told me. This is at the foundation of the theory, and you are plainly hiding from it.
Nick,
I’m seeing a lot of personal attacks and attempts at character assassination on ID proponents. Can you please cite any papers in support of your claims, especially pertaining to the claim that the Darwinian mechanism can produce copious amounts of complex, specified information? Thanks.
Well Nick, as to:
And yet we find, at least, 1000 ORFan genes in humans alone that are not found in any other species. Completely unique ORFan genes that were thrown out of the human gene count, in one study, simply because the neo-Darwinists doing the study could not find the ORFan genes in any other species:
This following article, which has a direct bearing on the 98.8% genetic similarity myth, shows that over 1000 ‘ORFan’ genes, that are completely unique to humans and not found in any other species, and that very well may directly code for proteins, were stripped from the 20,500 gene count of humans simply because the evolutionary scientists could not find corresponding genes in primates. In other words evolution, of humans from primates, was assumed to be true in the first place and then the genetic evidence was directly molded to fit in accord with their unproven assumption. It would be hard to find a more biased and unfair example of practicing science!
The sheer, and blatant, shoddiness of the science of the preceding study should give everyone who reads it severe pause whenever, in the future, someone tells them that genetic studies have proven evolution to be true.
If the authors of the preceding study were to have actually tried to see if the over 1000 unique ORFan genes of humans may actually encode for proteins, instead of just written them off because they were not found in other supposedly related species, they would have found that there is ample reason to believe that they may very well encode for biologically important proteins:
In fact it turns out that the authors of the ‘kick the ORFans out in the street’ paper actually did know that there was unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore it in favor of their preconceived evolutionary bias:
Moreover the ‘anomaly’ of unique ORFan genes is found in every new genome sequenced:
As well, completely contrary to evolutionary thought, these ‘new’ ORFan genes are found to be just as essential as ‘old’ genes for maintaining life:
I would like to reiterate that Darwinian evolutionists cannot account for the origination of even one unique gene or protein, much less the over one thousand completely unique ORFan genes found deeply imbedded within the 20,000 genes of the human genome:
As to this lie, ahem, I mean comment of yours:
Yet contrary to your deceptive claim of ‘quite minor disagreement in a very tiny region of Possible Tree Space’. The truth is;
You know Nick your link on point 3 doesn’t work, which is just as well since I am fairly certain that it is a sequence comparison instead of an actual demonstration of the almighty power of evolution, further down Your light dark colored moth example of preexisting information variation within kind is a friggin joke as to demonstrating the power of darwinism to create anything new. But hey Nick, I try to be a fair guy, so let’s see if i can help you see what an actual SCIENTIFIC demonstration of Darwinian evolution might actually look like:
The search for the ‘Edge of Evolution’; What can neo-Darwinism really do???
Four decades worth of lab work is surveyed here:
Michael Behe talks about the preceding paper in this following podcast:
How about the oft cited example for neo-Darwinism of antibiotic resistance?
That doesn’t seem to be helping! How about we look really, really, close at very sensitive growth rates and see if we can catch almighty evolution in action???
Shoot that doesn’t seem to be helping either! Perhaps we just got to give the almighty power of neo-Darwinism ‘room to breathe’? How about we ‘open the floodgates’ to the almighty power of Darwinian Evolution and look at Lenski’s Long Term Evolution Experiment and see what we can find after 50,000 generations, which is equivalent to somewhere around 1,000,000 years of human evolution???
Now that just can’t be right!! Man we should really start to be seeing some neo-Darwinian fireworks by 50,000 generations!?! Hey I know what we can do! How about we see what happened when the ‘top five’ mutations from Lenski’s experiment were combined??? Surely now the Darwinian magic will start flowing!!!
Now something is going terribly wrong here!!! Tell you what, let’s just forget trying to observe evolution in the lab, I mean it really is kind of cramped in the lab you know, and now let’s REALLY open the floodgates and let’s see what the almighty power of neo-Darwinian evolution can do with the ENTIRE WORLD at its disposal??? Surely now almighty neo-Darwinian evolution will flex its awesomely powerful muscles and forever make those IDiots, who believe in Intelligent Design, cower in terror!!!
Now, there is something terribly wrong here! After looking high and low and everywhere in between, we can’t seem to find the almighty power of neo-Darwinism anywhere!! Shoot we can’t even find ANY power of neo-Darwinism whatsoever!!! It is as if the whole neo-Darwinian theory, relentlessly sold to the general public as it was the gospel truth, is nothing but a big fat lie!!!
Nick,
Nearly anything “interesting” requires, at a minimum, both a physical and behavioral change. It’s not an absolute truth, but you could spend the rest of your life counting examples.
In a nutshell, living organisms have things and use things. They cannot use what they do not have, and, according to theory, they do not pass on modifications which are literally useless. You’re whistling along in your “happy day” scenario where phenotypic changes can accumulate without any cooperation from the rest of the organism, including its behavior. Theory, this is reality. Say hello.
Would you care to explain how any such developments could result from single mutations? You haven’t even attempted to explain how any of them arose from multiple mutations. You just compare two genomes and bridge the gap with assumed mutations and selection.
Before I distract from the question, please explain yourself. Please provide a relevant example of something “interesting” that happened from a single mutation and that can reasonably be extrapolated to all other diversity. And if you have time explain why it isn’t in every high school science book between the peppered moths and whale tales.
But, but…you JUST admitted that mutation-by-mutation detail was not required to produce a plausible pathway, when you conceded that it was reasonable to think that natural evolutionary processes could move the amount of mucilage secretion up and down. Can you make a consistent argument for two consecutive posts please?
Then quote my model for the origin of the Venus flytrap, and reference it with a link to the original, like decent posters are supposed to. I’m not going to re-type it AGAIN just because you’re too lazy to look it up and you prefer to just assert it doesn’t exist.
bornagain77 writes/spams:
bornagain77 — dude! Where do you get this stuff?? We discussed this paper in my seminar at Berkeley, it has NOTHING to do with tree incongruence statistics at all!
I know exactly what the paper is about — do you, or are you just posting massive amounts of random spam? Why should I even talk to you if you are not a serious discussant and just a link spammer?
Unless you go look up this paper, read it, and give a decent explanation of what it is about, and tell me why you posted it, I’m going to go back to ignoring your posts completely. Hint: it involves the difference between exponential distributions and normal distributions.
Cheers!
Nick
PS: Other random quotes, some of them ancient and outdated, about congruence don’t mean squat unless they are statistical statements. Statistics of tree congruence:
http://www.talkorigins.org/faq.....ruent.html
ORFans — these will occur at a reasonable frequency at random when you have billions of nucleotides as in humans, there is no particular reason to think they are functional. All you need is a start codon followed by a stop codon. Furthermore, the human genome is more completely sequenced than most other “complete” genomes (genome sequencing is never literally 100% complete), so there may be a few cases where the region just hasn’t been sequenced in chimp or monkey yet. But most of them are artefacts.
The bacterial case which Ochman writes about is completely different from the human case, since many bacteria have no close relatives sequenced, and they acquire genes from the environment etc., although many of those ORFans may be artefacts as well.
Nick,
My position is consistent. I’m sure that a single genetic change can move the amount of mucilage secretion up and down.
I do not extrapolate from that every variation in all of biology. I don’t demand proof that you can glue two popsicle sticks together. But if you tell me you can make a space shuttle out of them I’ll be a bit more demanding.
That was a rather weak attempt.
What? I’m telling you that you’ve never posted or referenced any detailed, meaningful explanation, and you want me to link to it? Link to what? I can quote it for you in its entirety:
Let me repeat what you are trying to avoid: You claim that an accumulation of individual genetic changes can, over time, evolve a glue trap into a fly trap, or something else into something else.
But your proverbial ‘mountain of evidence’ contains anything but a detailed account of such a transformation. I’d be impressed if you just made something up. What makes you think that a model or a narrative covers that base?
You cannot with any degree of certainty attribute countless changes to a mechanism that apparently has never been observed well enough to document or test.
The challenge is so simple, and with every post you try to distract from it. I don’t think you have anything, and you make my case with every post.
You lose:
http://www.uncommondescent.com.....ent-402002
http://www.uncommondescent.com.....ent-402110
Read the papers and explain why the evolution of a snap trap from a glue trap is implausible, or else you haven’t got a case at all. I’m not going to type them out for you, sorry.
ScottAndrews, you will never get a “detailed account of such a transformation” from Nick. He is not an engineer and doesn’t think like one. Nick swoons very easily when he sees sequence similarities or homologous proteins (like with the bacterial flagellum). Since blind purposeless processes obviously brought everything about, there is no point is discussing the actual details of the transformation. Noting a few similarities between organisms is wholly sufficient to solidify the built-in confirmation bias.
Nick,
You can’t seem to answer the question without changing it. I’m asking for evidence that this is a valid explanation, and you’re backtracking to “plausible.” What is plausible? Plausibility is subjective.
You express certainty that variation and selection are the engine of diversity. You have to be pretty sure of something to mock anyone who disagrees. But pressed for examples, observations, or specifics you present some toothless corroboration and ask, ‘Isn’t it obvious? Isn’t is plausible?’ It’s neither.
And what’s up with linking to one of your previous posts in which you proclaim that you explained everything in another previous post? I have a sense of humor, but I don’t think you’re joking. It’s turtles all the way down.
Michael Flatley couldn’t dance like this. It’s pointless but it’s fun to watch.
Eric,
How true. I don’t know how many times people including Nick have linked papers which supposedly detail the evolution between two organisms, but in reality only mention a few genetic differences.
One of my favorites showed a difference in how forelimb growth was regulated between rodents and bats. There is never an attempt to explain the differences. What varied? Why was it selected? Why do I have a bird feeder outside my window and not a bat feeder? The answer is always ‘well-known evolutionary’ processes. Read the papers referenced by the papers I reference which explain why it’s plausible. Come back tomorrow and don’t look behind the curtain.
Nick as tempting as it is to have you completely ‘ignore’ me (since you don’t really listen to anything I put to you anyway), alas I cannot let you deceive again as you have here;
Here is the entire article that you incredulously stated: ‘it has NOTHING to do with tree incongruence statistics at all!:’
You can lead them to the water, but you can’t make them drink…
Further notes on tree incongruences:
Thus Nick no matter how you try to twist and turn the evidence to fit your bias, the fact is that the evidence itself is what is falsifying your claims for neo-Darwinism!!! You can get us names and get mad all you want, but the simple fact is that it is the evidence you should be mad at NOT US!!!
Our knowledge is a receding mirage in an expanding desert of ignorance.
– Will Durant
bigej,
Then you must have missed ba77’s intro to his comment at 2.1.1.1.4:
paragwinn, care to quote Nick’s comment directly preceding that comment?
But alas paragwinn, perhaps we can get past all this mud slinging, as if mud slinging is ever the high road to take, and focus directly on the science as bbigej suggested, Perhaps you care to take up bbigej’s challenge to ;
paragwinn, produce such evidence and you can forever silence us ‘IDiots’!!!
That’s not the research article, it’s the news article summary.
And either way, it has NOTHING to do with incongruence between phylogenetic trees! Do you even know what incongruence means? They used phylogenetic trees to do the study, for godssakes!
Bolding random parts of a news article about a research paper you don’t understand is not an argument. These kinds of shenanigans are why I mostly just ignore your posts, and why the scientific community will definitely, and rightly, never take the kind of stuff you put out seriously.
Here’s what the article was actually about — using phylogenetic trees to test whether the most common mechanism of speciation was:
1. A matter of gradually building up many small changes — which might be expected if natural selection of a long series of mutations was the major cause of lineage-splitting.
2. A matter of single, rare events — which might be expected if dispersal to new regions was the major cause of lineage splitting, e.g. when a species on rare occasions gets over a mountain range, out to a remote island, etc.
#1 predicts that the lengths of the branches between nodes on the phylogenetic tree will have a normal (bell curve) distribution, since if you add up the waiting times of a large number of exponentially-distributed events, you get a normal distribution.
#2 predicts that the lengths of the branches between nodes on the phylogenetic tree will have an exponential distribution.
They found statistically more support for #2. Since a lot of biologists have had the opinion that geographic separation is the most common cause of speciation, this tends to support their position.
There are various criticisms one can make of the study, since e.g. estimating branch lengths is nontrivial, but that’s neither here nor there.
In short…what am I, as a scientist, supposed to think about the shenangians you are pulling here? I know you’re not doing it dishonestly, you’re doing it out of the confidence that you’re correct, and your eagerness to show it — but that’s almost worse! Imagine what it looks like to a scientist who is already predisposed to dislike religion. Here’s a guy who calls himself “bornagain77”, who goes around telling people that a major scientific theory is a total fraud, yet he can’t even get the first thing correct about a recent scientific paper, and his doubling-down on the mistake indicates he doesn’t even care enough to double-check his claim once he is criticized about it.
I’m just amused, because I’ve seen such shenanigans so many times from creationists, but a lot of scientists get pretty darn ticked off at the abuse of their work and their field by people who have high confidence, but no idea what they are talking about. This, not atheism, is what makes so many scientists so strongly opposed to creationism/ID. That and the fact that other creationists/IDists don’t correct such mistakes, which are being made all the time.
And, if the goal is to convert people to evangelical Christianity, imagine how your behavior looks from the scientists’ perspective. Apparently, becoming born again involves throwing away your brain, naively misinterpreting the hard and careful work of scientists, and loudly proclaiming to the world that the scientists are wrong, when you don’t even know what you are talking about. That’s about the last thing that will ever appeal to a scientist, or to anyone who values science.
Creationists are one of the biggest impediments to successful apologetics that exists in the modern world.
Like when a pair of monkeys is prevented from mixing offspring with the rest of their population by the ocean they just made a raft and sailed across? I believe the phenomenon is called genetic drift.
Nick,
Apparently the diversity of life via mutation and selection boils down to an extrapolation through which the rest of the evidence is filtered. If there’s anything more I’m never going to get it out of you. (Thank you for leading me to an empty ditch and waiting for me to drink.)
That’s quite a stretch of the imagination. Here’s my extrapolation. I know that even hard-working scientists blow it once in a while. It’s even easier in a field that lends itself to making up unverifiable stories. We’ve seen contradictory research on whether we should brush our teeth up and down, sideways, or in circles. It was once common knowledge that bacteria could never survive in our digestive tracts. Excess dietary calcium caused kidney stones. And so on.
These people were not idiots. And these examples, while common, do not represent of pattern of scientific incompetence.
They do however demonstrate a point. Scientists can be dead wrong, individually and collectively.
That does not indicate whether an individual or group is right, wrong, or somewhere in between in any particular case. It simply indicates that such ‘wrongness’ is by no means rare or unheard of.
So you may choose to extrapolate that limitless apparent but unintended ingenuity and engineering can arise from the tiniest of variations. And apparently you gain confidence from having the majority of the scientific community behind you.
But, based on numerous examples, it’s also easy to conceive that scientists, both individual and communities, can sometimes be off in left field, regardless of their passion and dedication, and that this is likely one of those cases.
Which is a greater stretch of the imagination? The known phenomenon of group-think applied in this particular case, or tiny step-by-step variations leading lizards to grow wings, use them, and discover migration routes from North America to South America by way of air currents over the eastern Atlantic which would get them killed unless they already knew where they were going?
Your extrapolation is a far bigger reach. And that’s just based on considering which possibility is simpler and more plausible. It’s not even factoring in that the science itself is crap.
Nick, the crushingly beautiful thing about this study, against neo-Darwinism, is the incongrence with EACH individual tree to the theory of neo-Darwinism!!! We, in fact, despite attempts to dance around the implications, have 101 individual witnesses each testifying that the prevailing “TREE” view of a gradually branching neo-Darwinian ‘tree’ of gradual change into new species is completely wrong!!!., In fact this study, despite your name calling and stonewalling denial to the contrary, directly contradicts your initial comment, ‘quite minor disagreement in a very tiny region of Possible Tree Space’, for the plain fact is, no matter how ‘scientific you perceive yourself to be, that we have 101 individual ‘tree’ witnesses testifying that there is quite a major disagreement between Darwinian theory and the ACTUAL evidence. The other studies I listed, that you merely hand waved off as old and outdated (even though some are recent), are in fact the icing on the cake and do you no good whatsoever, for they show that when trees are compared to each other, that, as one study put it, 50% of sequences will give you one history and 50% of sequences will give you another. Thus Nick, though you belittle me, and every one else who has the audacity to question the almighty power of evolution, the fact is you have no help from any study, whether they are done with individual trees or whether they are done by comparing trees with each other. Yet instead of you realizing that this study provides another line of evidence against neo-Darwinism, you attack me and then rationalize the results away as if they mean nothing, instead of dealing with the evidence forthrightly, as would anyone who was a true scientists would do, but you, apparently, are not so much concerned with calmly and cooly evaluating the evdence and coming to a correct conclusion as you are in protecting your beloved atheistic worldview, evidence be damned if it gets in they way!!!
Nick as to this rationalization of yours of the study:
Yet these following studies find that this gut reaction rationalization of yours is severely wanting:
This following article reveals how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:
further notes:
So apparently you don’t even know what the word “incongruence” means, when referring to phylogenetic trees. I even put a link up that explained it. Wow. Just…wow.
Anyone want to defend bornagain77’s use of this paper? [birds chirping]
Nick, now in realizing your superior intellect, and how you have humbled this IDiot with the massive molecular fluctuations of your brain that produce such superior thoughts of truth (though in my ‘IDiotness’ I still can see no reason to presuppose why your ’emergent’ thoughts, from molecular fluctuations in your brain, should correspond to the truth, nor why you should think your fluctuations of emergent thought should not give you a completely different truth tomorrow), but anyways,,,, in being so humbled by such brilliance of molecular fluctuations of your brain, I was wondering if you could perhaps find the time to formally falsify Abel’s null hypothesis? (There’s a million dollar prize in it for you) You could probably do such trivial stuff while your brushing your teeth, or whatever,,, and just think of all the time you will save in the future by not having to tirelessly defend what seems to be so clearly evident to you, but is so clearly deficient to us poor lowly IDiots who were not blessed with such lucky configurations of brain molecules as to figure out why random configurations of material molecules never seem to generate functional information (except in our brains of course! 🙂 ).
Music:
Do they define “nontrivial”? The classic pattern is that creationists declare X can’t evolve, evolutionists show how X evolves, then the creationists declare X trivial and move to Y.
Guess who?
It makes even more sense now.
Why would I want to silence you? You’re too entertaining.
As far as I can tell, the main complaint is that a comprehensive, detailed account of a specific evolutionary event/process is not provided.
Is it possible to provide those details with the design inference as the tool?
Nick Matzke:
They cannot do that if tey do not know the genes involved.
Also if tey ent into a lab and produced a snap-trap from a glue-trap that would help their case. And without that they don’t have any science…
Wring again, Nick.
1- Neither Creationists nor IDists say “X can’t evolve”
2- Evolutionists NEVER show how X can evolve via blind, undirected chemical processes- they just say it- as in they use teir imagination to “show” how it can evolve.
IOW Nick evos = wankers.
With evos you can’t even lead them to water…