Here is the abstract from a Nature Review: Genetics paper:
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
Many years ago, I predicted that modern genome sequencing would eventually prove one side of the argument to be right. This review article indicates that ID is the correct side of the argument. What they describe is essentially what ID scientist, Michael Behe, has termed the “First Principle of Adaptation.” (Which says that the organism will basicaly ‘break something’ or remove something in order to adapt) This paper ought to be the death-knell of Darwinism, and, of course, “neo-Darwinism,” but, even the authors who report this new “perspective” have not changed their Darwinian perspective. Somehow, they will find a way to tell us that the Darwinian ‘narrative’ always had room in it for this kind of discovery. As Max Planck said, and I paraphrase, “a theory does not prove itself right; it’s just that the scientists who opposed it eventually die.”
Here is basically the first page of the article (which is all I had access to):
Great attention has in the past been paid to the mechanisms of evolution by gene duplication (that is, neofunctionalization and subfunctionalization). By contrast, gene loss has often been associated with the loss of redundant gene duplicates without apparent functional consequences, and therefore this process has mostly been neglected as an evolutionary force. However, genomic data, which is accumulating as a result of recent technological and methodological advances, such as next-generation sequencing, is revealing a new perspective of gene loss as a pervasive source of genetic change that has great potential to cause adaptive phenotypic diversity.
Two main molecular mechanisms can lead to the loss of a gene from a given genome. First, the loss of a gene can be the consequence of an abrupt mutational event, such as an unequal crossing over during meiosis or the mobilization of a transposable or viral element that leads to the sudden physical removal of the gene from an organisms’ genome. Second, the loss of a gene can be the consequence of a slow process of accumulation of mutations during the pseudogenitzation that follows an initial loss-of-function mutation. This initial mutation can be caused by nonsense mutations that generate truncated proteins, insertions or deletions that cause a frameshift, missense mutations that affect crucial amino acid positions, changes involving splice sites that lead to aberrant transcripts or mutations in regulatory regions that abolish gene expression. In this Review, the term ‘gene loss’ is used in a broad sense, not only referring to the absence of a gene that is identified when different species are compared, but also to any allelic variant carrying a loss-of-function (that is, non-functionalization) mutation that is found within a population.
Here, we address some of the fundamental questions in evolutionary biology that have emerged from this novel perspective of evolution by gene loss. Examples from all life kingdoms are covered, from bacteria to fungi and from plants to animals, including key examples of gene loss in humans. We review how gene loss has affected the evolution of different phyla and address key questions, including how genes can become dispensable, how many of our current genes are actually dispensable, how patterns are biased, and whether the effects of gene loss are mostly neutral or whether gene loss can actually be an effective way of adaptation.
So, let’s translate what they’re saying here: “speciation” (their term is “phenotypic adaptation”) is the result of a LOSS of INFORMATION! This points, of course, to the “front-loading” of the LCA of the various branches of the so-called “Tree of Life.” Absolute bad news for Darwinism. We no longer say: “Another day; another bad day for Darwinism.” We now say: “Another day since the time Darwinism was disproved.”
This is what one of the authors has to say in an interview:
“The genome sequencing of very different organisms has shown that gene loss has been a usual phenomenon during evolution in all life cycles. In some cases, it has been proven that this loss might mean an adaptive response towards stressful situations when facing sudden environmental changes” says Professor Cristian Cañestro.
“In other cases, there are genetic losses –says Cañestro- which even though they are neutral per se, have contributed to the genetic and reproductive isolation among lineages, and thus, to speciation, or have rather participated in the sexual differentiation in contributing to the creation of a new Y chromosome. The fact that genetic loss patterns are not stochastic but rather biased in the lost genes[pav: IOW, this is where you’re going to find the genomic differences between species you compare] (depending on the kind of function of the gen or its situation in the genome in different organism groups) stresses the importance of the genetic loss in the evolution of the species.
There you have it: “evolution” through “gene loss.” I.e., “evolution” through “loss of information.” Evolution does not PRODUCE “information”; it DESTROYS “information”. You can read about in the book: “Genetic Entropy.”
In sum: the war is over, and we won! Congratulations everyone!
“But this is exactly what [insert favourite of Darwin, evolution, new-Darwinism, neutral theory, etc, etc] predicted”
…..
I’m sorry PaV, but why does a gene which fails to function because of physical forces acting upon the gene, and then the resulting phenotype being expressed differently, prove Intelligent Design? Couldn’t the designer fabricate a stronger template to prevent this error accumulation?
Or rather, with gene loss, and the resultant new expression, why can’t this new expression be beneficial to the individual?
rvb8 –
“Couldn’t the designer fabricate a stronger template to prevent this error accumulation”
Fairly irrelevant. You could take any design and say, “couldn’t this be done better?” Just because it could have (or you imagine it could have) has no real bearing on whether or not something was designed. By that criteria, we have definitive proof that there was no one on the design team for Windows.
“Or rather, with gene loss, and the resultant new expression, why can’t this new expression be beneficial to the individual?”
It totally can be, but it is totally beside the point.
The point is, if evolution is about gene *loss*, then that indicates it *isn’t* about the gain of genes. If the observed pattern is that we *lose* information, then this isn’t a good theory of where it comes from. The core of Darwinism says that life started information-poor and increased in information-richness over time by accumulation. ID, on the other hand, says that we *started* with fully-developed information sources.
If the process of evolution is merely the getting rid of existing information, then ID was the one that was right.
Evolution is not “about gene loss.”
Are you guys completely incapable of detecting PaV’s sarcasm?
He’s merely playing down another mechanism of evolution and even trying to spindoctor it into “support of ID.”
Unfortunately for you guys, this review paper in no way helps ID, and neither does PaV’s misrepresentations of actual science.
Alicia C:
Dear Alicia, I’m not being sarcastic. The war is now over. Your side has lost.
What this review article presents is the complete ANTITHESIS of what Darwinian evolution should look like.
Let me put it another way: Darwinism couldn’t have been MORE wrong.
As to my “misrepresentations of actual science,” please consult Dr JDD’s post.
rvb8:
As I mentioned in my response to Alicia, the paper I’m quoting presents results that are: (1) the complete opposite of what Darwinism should look like; (2) confirmation of what a principle made by an ID theorist; and (3) confirms what a supporter of ID has written in a book.
There you have it: complete rejection of Darwinian expectations, and, simultaneously, confirmation of what ID thinking people have stated is going on.
It’s not too late to switch sides.
Gene loss is just another mechanism of evolution. It is not THE mechanism of evolution. You guys love to blow up research that you don’t even understand.
Alicia:
Your comment makes clear that it is you who do not fully understand the implications of this review article.
It basically says that what Darwinists believe is “evolution”– you know, the “origin of species”–is driven by a “loss” of information, not a steady, gradual build-up of information. IOW, there is no foundation for Darwinism.
But, of course, if an “intelligent agent” is involved, this “information” is infused, and this discontinuous infusion of “information” can also include mechanisms which allow for “adaptation” through a gradual LOSS of the infused, phyla-level “information,” as in NGE. This paper is fully consistent with ID; it is the death-knell of Darwinism.
The war is over: we won! The only thing that remains is for a declaration of surrender to be ‘signed.’ You can be the first to sign!
The Adder’s Tongue fern has 1200 chromomes, the Human 46, the kingfisher 132, Great Apes and Hares 48, the Horse 64 etc. The thing is, the complete arbitrary nature in which these numbers vary, with a sea slug having maybe 400, and mushromm several hundred, and then an eathworm and Tibetan Fox sharing 36, tells me clearly there is no design.
This utter randomness in the gene count, from the supposedly highest ‘human’, to the lowest bacteria points to chaos, not design.
rvb8:
You’ve succeeded in making a “mountain out of molehill.” There could be lots of reasons for those numbers; meanwhile, the astronomically, infinitely small probabilities associated with even an average size de novo protein is enough to invalidate Darwinism.
You “strain gnats, and swallow camels.”
PaV. Please.
Gene loss is nothing new. They are saying it’s been over-looked and has an important role in evolution, just as gene duplication, mutations, transposable elements, chromosome rearrangements, etc. all do. No where does it say that “evolution is driven by a loss of information.”
It’s funny you think you can claim the research paper says “this” and “that” when you have already admitted to not even having access to the actual paper.
Alicia:
Please. Of course gene loss is nothing new.
As to it’s saying “evolution is driven by a loss of information,” they would deny this; however, that is the import of the paper.
Here’s what’s new: extensive sequencing of genomes! I said 7 or 8 years ago, at a time when sequencing was becoming quicker and less expensive, that the comparison of genomes would either confirm the Darwinian view, or, that of ID.
The evidence is in: information actually drives speciation, a complete inverse of what neo-Darwinism expects. It’s the nail in the coffin.
Holler all you want, but, the war is over: and we won!
Alicia:
Here’s what one of the authors has said in an interview:
Here’s my translation:
“The view up until now is that to evolve means a gain in complexity, a gain in genes. This is what was thought when they sequenced the first genomes, of the fly, of worms, and of human beings. However we have seen that this isn’t how things are. The majority of our genes can be found in sea anemones. Our common ancestor had them. It’s not that we have gained genes, rather, it’s that they have lost them. Genetic complexity is ancestral,” said Canestro.
The war is over: we won!
The war is over and I’d rather say it is everybody’s loss. If gene loss is allowed to go on for much longer, kids will be born without genes.
Alecia:
Lets make this easy for you to understand. To go from a fresh water drinking land animal, to a salt water swimming 15 000kg whale, would require an immense increase of novel genetic information. This paper indicates evolution by gene loss, which is counter intuitive the usual Darwinian paradigm.
Time to dust of your white flag.
I predict that creationists will have a field day with this new discovery as it seems to validate one of their main points they have been making for years. Evolution works, but the progression is not in the right direction needed to see a single cell turn itself into a human being. I haven’t read the paper either so this is simply based on the OP.
Losing genes and breaking genes is simple. No one argues that evolution can do this. We are all in total agreement on that point! The evidence for it is incontrovertible.
However, the evidence for evolution in the opposite direction is much more theory driven and unclear.
From the website of the ‘Universitat de Barcelona’:
PaV,
Thanks for drawing attention to this remarkable scientific finding.
Without getting into much detail, the message is clear. The evolutionist claim regarding the natural development from simpler forms to more complex is under threat. Fortunately, the scientific process is free from emotions that overload some of the responses from our Darwinist friends 🙂
Now the question is, where did the initial complexity come from?
Game over.
As long as they stay within lineages of a specific species, they are correct in their conclusion that gene loss was integral to adaptation to specific environments
IMHO, where they go off the rails in the study is where they try to extrapolate the loss of genetic information witnessed within lineages of a specific species to try to claim that gene loss was integral to macro-evolution between species.
The large percentage of ORFan genes found in every new genome sequenced, by itself, refutes that notion.
Of related note to the ‘rotting Y chromosome’ hypothesis they alluded to:
The review is interesting (you can see it all via the naughtiness that is sci-hub), but it doesn’t put deletion into context compared to other mechanisms of genomic evolution. So gene duplication (for example) could be much more important and prevalent.
Declaring that the war is over because of this could be like saying that the Golden State Warrior are NBA champions because they scored 89 points in game 7.
The main idea of the paper is that gene loss is an important evolutionary force, just as gene duplication, mutations, transposable elements, chromosome rearrangements, etc. all are.
Period.
There is no massive overthrow of evolutionary thought, as you would like to believe. Don’t you think more of your friends would be jumping up and down and stomping their feet if it was?
Sorry to burst your bubble.
Bob and Alicia:
Almost all mutations are deleterious. When you compare species, you find de novo genes, which, probabilistically, cannot be explained, and is far beyond anything that gene duplication can explain.
When you add to this the growing body of knowledge spawned by sequencing that tells us gene loss is a prevalent method of speciation, then little is left of Darwinian notions.
When I say the war is over, I mean that Darwinism doesn’t have a leg to stand on. But you can’t tell that to Darwinists. So, it will probably take 20 years for this latest finding to sink in.
But, watch out, because the ENCODE project still continues, and they have a plan for elucidating function throughout the genome. And then what?
No junk-DNA; pseudogenes that have regulatory function; epigenetics demonstrating the tremendous dialougue between environment and genome. No, the war is over.
BTW, I left out the whole new area of transposons, which, as we know, have a non-random character.
Almost all mutations are deleterious?
So humans all have identical genomes?
How have scientists been altering the genome of organisms and cells for years without them all immediately dying?
“de novo genes, which, probabilistically, cannot be explained”
What about the explanations we already have for de novo genes? Are we ignoring those?
Please, you think encode is going to find function in the entire genome? They won’t even come close.
And what happens when they find that some of these functions are important for evolution, and not necessarily the individual organism? Are you guys going to count those?
“explanations we already have for de novo genes?”
Care to share?
Just go onto pubmed and search “de novo genes”
Do I need to walk you guys through everything?
Thanks for the non answer. Typical
It took more typing and clicking to post that comment than to go to pubmed and search “de novo genes”
Just another classic case of a creationist not wanting to learn.
I have neither the time nor the patience for what probably amounts to a literature bluff from Alicia. Is anyone familiar with these “explanations” and what is your opinion.
Right, instead of doing a simple literature search, you decide to ask the most unscientific community on the internet about….science.
I would expect nothing less from UD.
RexTugwell, The so-called ‘explanation’ for new genes from Darwinists is just the same ole hand-waving just-so story that Darwinists are notorious for whenever a finding contradicts their theory. (which is often)
Alicia Cartelli, since you are so concerned with being properly grounded in science, perhaps you would like to lay out the precise falsification criteria for Darwinian evolution so as to establish it as a testable hypothesis that is firmly grounded in science?
RexTugwell:
25, 27 and 29 must be the most embarrassing ‘triplet’ of posts ever seen on the internet.
Alicia Cartelli, It took more typing and clicking to post that comment than to go to pubmed and search “de novo genes”
Just another classic case of a creationist not wanting to learn.
We just want to articulate using your words . How de novo genes are well understood . That’s the insertion that you made . We don’t feel that they are well understood , So it’s not for us to make your case. So we just want you to back that up . Can you ?
Hahahahaha Dr Behe was right… again!
Many thanks, BA77. Now was that so hard, Alicia?
@Seqenenre: Not so embarrassing when my suspicions are ultimately confirmed. Nice try though. Maybe you’re willing to make a case for known mechanisms of de novo genes. Hmmm?
@Rex Tugwell:
Thanks for the non answer. Typical
I have neither the time nor the patience for what probably amounts to a literature bluff from Alicia. Is anyone familiar with these “explanations” and what is your opinion.
I used to love cartoons but then I grew up.
Seqenenre
Hi
There are pub med papers on di novo genes. The challenge for all the papers is identifying a mechanism that can account for their origin within reasonable population sizes and generations. According to Mychael Lynch’s paper in 2010 it takes over 1 million generations and a population size of 10^11to fix an adaption requiring 5 specific mutations. So based on this how does a di novo gene arrive in a human that is not in a chimp that requires more then 5 specific mutations? This is a very real and unresolved problem for the theory of common decent. The genome is an organized sequence and sequences have almost unlimited possible ways of being organized. How they get organized into a gene coding sequence is quite a mystery.
So.. what’s the argument here?
At the moment it reads like
1. Gene loss can be adaptive
2 …
3. also de novo genes are common and mutations are bad
4 ….
5 Victory
PaV @ 22 – I see you don’t rise to the challenge of asking whether gene duplication is more prevalent than gene loss.
I’m wondering what this probabalistic proof is that de novo gene can’t evolve.
I also don’t see ENCODE as a problem – the consensus is that they were being overly optimistic about function. I also don’t see why pseudo-genes having a regulatory function is a problem: evolution is messy, and whatever works will work. Epigenetic is just (!) the mechanism by which the environment affects gene expression, but we knew is did already – “G by E” isn’t controversial.
So, you can declare victory. If anyone notices, they’ll just shrug.
I have to mention this. YEC’s have stated for years that speciation is as a result of information loss. I think this paper vindcates them too.
Bob
Whatever works works….. hahahahahaha…. Darwinian evolution explains everything but really explains nothing….
Bob
It is not the consensus that disagrees with ENCODE it’s the dogmatists
Alicia posted, “the most unscientific community on the internet about….science.”
That is worthy of a heart felt ROTFL
Bob O’H
How would you evolve my cell phone number with a random unguided process? How about a number that would contact 1 of my 50 friends on my direct dial.
How would this change if phone numbers increased from 10 to 50 digits?
That adaptation is driven by loss of genetic information is overwhelmingly supported by many lines of evidence. Whereas the evidence that adaptation is driven by gain of information, as is presupposed in Darwinian thought, is slim to non-existent. The only reason this finding would even be controversial is because it flies directly in the face of Darwinian presupposition.
For prime example of how this flies in the face of Darwinian presuppositions we need look no farther than humans themselves.
Darwin presupposed that the Caucasian race was more evolutionarily advanced than the African race:
In fact, the belief that Caucasians were the most advanced race was an integral part of Nazi racial ideology.
Yet contrary to that Darwinian presupposition of racial superiority, which was at the root of so much misery in the world in WWII, the fact of the matter is that, genetically specking, Caucasians are actually genetically inferior to Africans. Whites are not genetically superior as Darwin and the Nazis presupposed.
In fact, Blue eyes, light skin, Blond hair and lactase persistence, contrary to what Nazis thought, are the result of the loss of genetic information, not a gain:
Moreover, contrary to what the Nazis believed about humans evolving into some sort of master race, the fact of the matter is that humans, all humans, are devolving instead of evolving:
The evidence for accumulating detrimental mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.
I went to the mutation database website cited by John Avise and found:
Again, The evidence for ‘devolution’, and/or adaptation by loss of genetic information is overwhelming. The only reason this is controversial is because it flies directly in the face of Darwinian presuppositions.
The Theory of Evolution is absolutely brilliant. It can predict anything in retrospect!
You see, evolutionary change in a genome has actually gotta be Oscillating Over Time(tm). It expands and contracts depending on the type of selective pressure or lack thereof.
Oh my! I feel the unmistakable tremor of a PhD eruption! 😉
-Q
Remember John Sanford and Genetic Entropy. –
“over 90% of the genome is actively transcribed”
“the genome has multiple overlapping messages”
“data compression on the most sophisticated level”
“more and more the genome looks like a super super set of programs”
“more and more it looks like top down design”
“the reality is everybody is mutant”
“the selection process really has nothing to grab hold of”
“so it’s kind of a trade secret amongst population geneticists,any well informed population geneticist understands man is degenerating”
“so in deep geological time we should have been extinct a long time ago”
“the human race is degenerating at 1-5% per generation”
http://idvolution.blogspot.com.....y-and.html
After rereading all the posts and PaV’s article again, and having visited several websites (Harvard, BBC, Wikipedia, Encyclopedia Britannica, Cambridge, Science Daily, Nature, etc), I have to conclude that PaV and bornagain77 have actually done it; they have successfully refuted and confounded Evolutionary Biology.
In a mere 700 words or so, s/he has overturned what Theodosius Dobzhansky explained as the unifying theory of life. Well done! Tell us about your Stockholm travel arrangements so that we can share in your success.
Bornagain77,
This data is child’s play for any Darwinist to accommodate!
It simply demonstrates how long humans have been evolving, since more evolved species obviously accumulate more mutations between Massive Evolutionary Upswings. 😉
-Q
rvb8, since Darwinian evolution is. in reality, a religion instead of a testable/falsifiable science, then there is no falsification that will ever be allowed to falsify Darwinian evolution in the minds of the faithful.
Theodosius Dobzhansky, whom you mentioned favorably, proves as much:
If you disagree with the fact that Darwinian evolution is a pseudo-scientific religion, instead of a testable/falsifiable science, then please present the exact falsification criteria that will allow an experimentalist to test its claims.
In fact, not only is Evolution not based on any known universal law, as other overarching theories of science are based upon known universal laws, (including ID being based upon the ‘law of conservation of information’), Entropy, a law with great explanatory power in science, almost directly contradicts Darwinian claims that increases in functional complexity and/or information can be easily had,,,
So rvb8 how exactly is one suppose to overturn a ‘scientific’ theory that doesn’t even a qualify as a testable scientific theory in the first place? Evidence is useless against such a ill-begotten contraption that is called Darwinian evolution!
The LAWs that prove the THEORY, thus making the THEORY fact:
“These laws,taken in the largest sense, being Growth with Reproduction; (I think living things follow these LAWs. rvb8) Variability from the indirect and direct action of the external conditions of life, and from use and disuse; (Another law. rvb8)a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms.” (so many LAWs here; desire for sex-more off spring-competition-success-more sex etc etc)
I’m sorry BA77 but your constant twittering on a subject already confirmed, and the absurd title of this piece are embarassments for your position, which, to quote Wolfgang Pauli is, ‘not even wrong’.
What is that gibberish you wrote? Are you drunk?
Moreover, Wolfgang Pauli was certainly no friend of ‘very irrational’ evolutionists:
Heh:) “that gibberish”, is from ‘The Origin of Species‘ you may have heard of it? Try reading it slowly. It actually makes a lot of sense, try this: living things like to reproduce, in many instances they even find the act fun. Having reproduced they next want to live. If the inherited traits of one living thing give it an advantage over another living thing, then that living thing will be more successful in sex.
Honestly, I don’tknow how to dumb down Darwin’s “gibberish” (Heh:)) any more.
So the law of ‘having fun’ by ‘wanting to reproduce’ and the law of ‘wanting to live’ form the basis of evolution in science? 🙂
Can you show me exactly where those constants/laws of ‘having fun’ by reproducing and ‘wanting to live’ are in the NIST table? 🙂
To repeat, there is no natural ‘law of evolution’ within physical science:
Moreover, the mechanism of random mutation that Darwinists imagine to be the ultimate creator of all life on earth is actually the primary reason why all living things eventually grow old and die:
And no, natural selection does not help:
Alicia C:
Yes. They’ve known this since the 60’s. Maybe you can read up on it.
I have no idea what you’re talking about. Please clarify.
Did I say they were “deleterious,” or did I say they were “deadly”? Your strawman argument will get you nowhere.
BTW, I have thalassemia.
But Darwinists have explanations for all kinds of things. But are they plausible? In the really important cases, usually not.
A portion of de novo genes are “novel” genes, and of considerable length. They are termed “novel” because they don’t match up with any annotated genes. How did these genes arise? What was the mechanism?
To put together a new protein of average length requires an improbability of more than 1 in 4^900, roughly, just to give a ball park figure. This is simply another way of saying that an average size protein cannot be made using random processes. It’s simply impossible. Everyone know this. But if you want to deceive yourself badly enough, you can believe the impossible happens.
They found some kind of function for what, 82% of the genome. And, they said that this percentage would rise. Why? Because some portions of the genome are expressed only for short periods of time during development, and, through improving their assaying techniques, they hope to confirm functions for those segments that, once development has ended, no longer function. So, it’s worse than you think.
Ask yourself this question Alicia: what will make me stop believing in Darwin’s theory? What does the answer to this question look like exactly?
Bob O’H:
Does gene duplication increase the information content of the genome? Does gene loss?
When will you recognize that that’s the way to argue with someone who holds the ID position?
Will the mechanism of duplication and subsequent degradation help? Can it bring about a “novel” gene? Answer: No.
Nucleotides are chemically interchangeable. Chemistry can’t explain the entirely “new” sequence of a “novel” gene. Random mechanisms can’t do this either. That leaves intelligent agency. Simple as that. And logically compelling.
The consensus now. And then when that consensus is completely undermined by evidence, the “new consensus” will be that you knew this all along, and that this isn’t anything new at all.
They were called “pseudogenes” because they didn’t have function. So, when you find function for this putative “pseudogenes,” then it looks like you didn’t properly understand what you were looking at.
This is not a very forthright answer. Of course everyone knew that the environment affected the genome: but not to the degree that it does. But what really makes your answer devious is the fact that you know that it is now known that epigenetics can have long-term inheritable effects. This is new; and a game-changer. Who are you trying to fool? Those looking in on this discussion?
Well, of course, Darwinists will shrug. They always do. No matter what evidence is discovered undermining the strange thinking they hold, they just shrug, invent some new amendment to their on-going narrative, and move on.
But your days are numbered. Why? Genome sequencing.
Darwinism, and neo-Darwinism, will never stand up to this test. ID, OTOH, will be vindicated.
It’ll just take a number of prominent evolutionary biologists to enter the pearly gates.
wd400:
Information, my dear wd400, information. Where does it come from? How does it arise?
“Almost all mutations are deleterious?”
I agree, but whether I agree or not is pretty unimportant, the facts are much more important. Large and random mutations in the genotype, producing new and radically altered offspring, and that this saltation is ruinous to the individual, is the accepted position in evolutionary science. Big and quick change at the level of saltation has always been accepted as harmful to life.
Why would you think this in any way undermines evolution, which is nothing, if not a fan of gradualism?
PaV,
Actually, both words start with the letters “de” and can easily be confused. Beside deleterious sounds much more serious.
That explains why Alicia asked the question
on the assumption that deleterious means deadly. Or is it delirious? Delicious? Desirous? Anyway, one of those long words. 🙂
Make sense now?
-Q
rvb8,
LOL!
C’mon you’re Spearshake or one of his sock puppets, right? You know—the guy who claimed he was an “expert” in statistics? Please say yes.
-Q
There was once a poster here in the early days who was called answersingenitals which I thought funny on many levels; sorry not Spearshake as I claim to be an expert in very little, and following the example of Socrates I am smart enough to know I know very little.
However large mutations are almost always, if not always deadly to the individual organism, I don’t need to be an expert to know this. And evolution is most certainly the science of gradualism by definition; why is this a silly statement?
rvb8,
Since saltation, by definition, is a big and quick evolutionary change . . .
Also look up punctuated equilibrium.
Look up the definitions for theory, law, and fact. Toss in hypothesis for good measure.
Are you sure you’re not Spearshake?
-Q
Saltation has never been documented in biology and my remarks concerning the gradualism of evolution remain.
‘Punctuated equilibrium’ is a theory within the theory of evolution put forward by Niles Eldredge and Stephen Jay Gould. It merely notes that ‘stasis’ is probably the normal order in evolution, punctuated by periods of increasing bio-diversity; Cambrian Explosion as one famous example.
Large mutations in genes producing freakish off spring are almost always, or even always deadly to the individual organism. This is not ‘saltation’, which along with Ken Ham’s absurd cladistic invention ‘kinds’, is never mentioned by serious scientists.
bill cole @46 – Is your phone number a de novo gene? I suspect not.
rbv8 @ 50 – bad news. I’m not sure this would fit under the rubric of any of the Nobel prizes. Literature, maybe.
Pav @ 58 – I see you are still punting on whether gene duplication is more prevalent than gene loss. You’re also still punting on the proof that de novo genes can’t arise.
Incidentally, I can’t use the information argument because I’ve never seen a definition of information from IDists that makes sense biologically. I’d rather not go round the “calculate the information for the flagellum” carousel again.
Oh, one thing:
I agree – that’s the wonderful thing about science, we often don’t understand what we’re looking at, so we figure it out.
Bob #66,
“I agree – that’s the wonderful thing about science, we often don’t understand what we’re looking at, so we figure it out.”
Yes, sure. But acknowledging a falsified hypothesis and moving on is way different from pretending the hypothesis still holds and modifying it as if nothing happened.
To reiterate, since Darwinian evolution is, in reality, a religion instead of a testable/falsifiable science, then there is no falsification that will ever be allowed to falsify Darwinian evolution within the minds of the Darwinian faithful.
http://www.uncommondescent.com.....ent-611045
No matter how contrary a finding may be to Darwinian claims, the contrary finding is simply crammed into the Theory of evolution by the addition of ad hoc ‘epicycles’ that try to ‘explain away’ the contradictory finding.
In fact, the only actual evidence ever witnessed for the unlimited plasticity of species predicted by Darwinian evolution has been within the theory itself. The theory is forever plastic, able to morph itself into whatever shape it needs to in order to avoid falsification by empirical observation!
Dr. Hunter puts the unfalsifiable situation with Darwinian evolution like this.
Dr. Hunter also has a site listing many of the fundamentally failed predictions of evolution:
The strength of a theory in science is in its predictive power. In fact, the predictions of General Relativity and Quantum Mechanics are tested to absurd levels of precision. Darwinian evolution is a joke in terms of its predictive power.
As mentioned previously, the reason why Darwinian evolution seemingly floats serenely above experimental reproach is that it has no falsification criteria.
Yet, despite the pseudo-scientific nature of Darwinian evolution, and despite the unwillingness of Darwinists to accept any falsifying evidence against their theory, as far as empirical science itself is concerned, Darwinian evolution is falsified in its most foundational claim. Specifically, Darwinian evolution is empirically falsified in its foundational claim that RM & NS can generate functional complexity.
relevant Feynman quote:
Pretty sure Behe called it “The First Rule of Adaptive Evolution” in his QRB paper.
Of related note:
Bmaque, my “insertion” was that scientists have come up with a partial explanation for how de novo genes arise and a simple pubmed search will get you a few recent articles right at the top of the list, feel free to even go into the references of those papers if you want to learn more.
So PaV, almost all mutations are deleterious, yet humans have thousands of genetic variations across the population? My point is that most mutations, though they may be slightly deleterious, are not immediately culled by natural selection. They can accumulate and contribute to evolution, like in thalassemia; what is deleterious in one environment, may be beneficial in another.
“an average size protein cannot be made using random processes.” Good thing no one is claiming this.
ENCODE’s results are very much up for debate, but I have no doubt that there is a good portion of unknown functionality in the genome. Depending on the perspective you take, organismal vs. evolutionary, you can get different amounts of function in the genome. I’m sure some evolutionary scientists somewhere at some point will even try to make the claim that because the genome is passed on to the next generation, the entire thing represents the potential for evolution and is therefore 100% functional. The scientific community is filled with people with slightly different ideas about each area of research, we feed off of controversy and constantly try to dispute each other, and yet we all seem to agree that evolution explains the diversity of species we see today.
What will make me “stop believing in Darwin’s theory?”
Well, first let’s put aside that it isn’t a “belief” and that it’s not even “Darwin’s theory” anymore.
But what would it take?
Hmm, let’s say take the number of things we have at least a partial explanation for in evolutionary biology, now take 1% of that, and that’s the number of things that if we had absolutely no explanation for or completely went against everything we know, then I would begin to question evolution.
“yet humans have thousands of genetic variations across the population?”
You fail to distinguish between non-random, i.e. ‘directed’, variation in humans and random mutations in humans. Directed mutations are non-Darwinian since they are not random (and since they still reduce overall information), and truly random mutations are overwhelmingly deleterious
Also of note:
Bob O’H:
In the article I cited, they downplay the role of gene duplication. I think that’s a good idea.
As to “de novo” genes arising, the more critical question is how do “novel” genes arise, those that cannot be connected to other known sequences. How do you explain it, Bob?
Who’s punting here, actually? Entropy is connected to information. All of science accepts this. Entropy is all about degrees of freedom. And, any nucleotide sequence has 4 degrees of freedom at each site. Do the math. It’s quite straightforward and easy.
But, of course, if someone chooses to be willfully ignorant, no one can help them “see.”
And, as EugeneS has already pointed out, when you “figure it out,” you should be willing to live with the consequences. But, no, the ‘Darwinian narrative’ must conquer all. So, it’s not falsifiable. Therefore, it is no longer a scientific theory, or even a postulate.
rvb8 @55:
“living things like to reproduce, in many instances they even find the act fun. Having reproduced they next want to live. If the inherited traits of one living thing give it an advantage over another living thing, then that living thing will be more successful at sex”
So why did sexual reproduction even evolve? What advantage does it offer? What advantage does needing 2 separate individuals to have sexual relations actually bring to the table? If evolution is about survival and most likely to reproduce then it should have stopped at bacteria. They are far better at it than any multicellular organism. Plus they can do it in all sorts of environments – hot, cold, high salt, low salt, oxide, anoxic….
Bob O’H
Both a phone number and a gene are sequences. The english language is also a sequence. This is why Richard Dawkins used a line of Shakespeare to simulate a protein search. By trying to visualize how difficult this is you will better understand the arguments that you are dealing with.
JDD,
Good quesiotn. I’d start with Sally Otto’s article here
Pav
Where? They mention more focus has been placed on duplication that loss, but that’s all. There is also quite a lot of discussion about the importance of duplication for gene loss (i.e. ancestral duplication followed by differential loss of daughter genes).
Wow so information is gained by losing it according to the Darwinists commenting here. Are we seriously entertaining this nonsense?
“In the article I cited, they downplay the role of gene duplication.”
If they really did do that, it shouldn’t surprise you, unless you have no experience in research, PaV.
Of course the researchers are going to make their work sound like the best thing since sliced bread while downplaying everyone else’s work. That’s what most research groups do, only to different degrees.
This site posts all the time about the current state of research, and for once you guys are actually right: it is, in part, a business.
Some people take it very personal when their world view is challenged.
PaV @ 73 –
Actually, they barely mention it, and make no comment on the relative importances. My guess is that they were asked to write a review about gene loss, and either decided comparing gene loss and gain would be too much, or had written something and were asked to take it out (to save space or not make the paper unwieldy).
By googling. And finding two papers that discuss just this. There are probably more too: these were from the first page of results.
Yes, I can count too. But so what? How does this relate to evolution, other than saying there is a very large genotype space? This is the problem I have – you can calculate these numbers, but I haven’t seen anything which suggests they’re meaningful with respect to evolution.
bill cole – lots of things are sequences. But they can be produced in lots of different ways. Frankly, I have difficulty seeing how phone numbers mate and recombine, especially when within a longer string of sequences.
“The war is over. We won!”
Whoever wrote this is very naive…
One example comes to my mind when Jesus performed a miracle and yet the Jewish scribes while acknowledging his miracle they were still seeking to kill him… Why?
Bob O’H
How are sequences like phone numbers and languages produced? What happens if they are changed randomly?
Bob O’H:
Ah, the old “I cannot imagine” defense. I could write a program in which phone numbers mate and recombine. Incredulity is not an explanation.
Alicia Cartelli:
Alicia’s posts are the best thing since sliced bread. Or at least they sound that way.
Dr JDD @74
The belief is that sexual reproduction offers a chance at genetic diversity that is not offered by asexual reproduction, thereby giving the offspring of sexual reproduction a better chance at dealing with disease and potentially harmful microorganisms.
That said, your point is completely valid. What we regularly see with evolutionary explanations for the arrival of some feature of biology is a description of some benefit it confers. The problem is that these sorts of explanations are blatantly teleological: Feature A evolved because it conferred advantage X. This might explain why a feature ended up being retained by natural selection after it arose, but it doesn’t explain why the complex feature arose in the first place, unless we want to assign intelligence to evolution (as has been recently suggested).
However, with regard to sexual reproduction, as you noted, it is far less efficient than asexual reproduction, so whatever advantages it confers, it carries some very significant evolutionary disadvantages as well. It offers an evolutionary advantage with respect to one set of considerations (genetic diversity), but an evolutionary disadvantage with respect to another set of considerations (reproductive success and larger populations). One wonders why the advantages should have outweighed the disadvantages in this case, since reproductive success is supposed to be the primary measure of fitness and main predictor of what traits will be passed on and fixed, while drastically reduced reproductive success and population sizes significantly decreases the potential for ongoing evolution in populations that rely on sexual reproduction. Meanwhile, asexually reproducing organisms may be more susceptible to disease and microorganisms, but they typically deal with these problems simply by having very large population sizes, and they are doing quite well to this day.
So, in short, the reasons given for why sexual reproduction has hung around are dubious at best, considering reproductive success is supposed to be primary measure of fitness, but these reasons do nothing to explain why or how it actually arose in the first place.
Hmmm…
If gene duplication doesn’t add information, then the duplicates have no information. But if a duplicate is lost, then information is lost.
That’s some sort of funny math there.
You are correct HeKS, asexual reproduction is far more successful than sexual reproduction. That is why some plants, and some fungi, and all archaebacteria, eubacteria, and protists are far more abundent and therefore evolutionarily successful than us.
It seems that everyone here is hell bent on asking, ‘then why are we here, why are we so special?’ If this is your question, then it sadly fails to understand Darwinian Evolution. We reproduce sexually because we inherited this method from ancient ancestors. The ligitimate question of why we went down this evolutionarily less efficient method, is what science is trying to answer. I have no idea what an ID question looks like, therefore ID also has zero answers.
Bacteria reproduce asexually, they were probably the first life, they have existed for billions of years, and it is absolutely certain that when we dissapear, or destroy the planet, they will still be happily chugging along, and definately producing random gene errors that will possibly lead to the next sentient beings.
Please type out your comment below.
Bob O’H:
If you read interviews of the authors, they seem to be very excited to have found a new way of looking at evolution, one driven by ‘gene loss.’
But, Bob, those are about “de novo” genes, not “novel” genes, per se. “Novel” genes are a subset of “de novo” genes, and they don’t match up to annotated genes; hence, their entire, sizable length have to be explained. Any ideas?
Isn’t the real “problem” that you’re accepting the “theory” of evolution as a “fact”? IOW, you say that when we look at organisms, their genomes are different, so we know that the ‘long odds’ against this happening are overcome. And, then, you attribute this to a purely materialistic mechanism. But that’s an assumption.
The only known “mechanism” of overcoming huge odds that we know of is the use of intelligence. That’s a big part of what Stephen Meyer argues in “Darwin’s Dilemna.”
You can’t use what you assume to prove that which is in dispute.
Arthur, this is from memory, and I only had the first two pages to look at:
I believe their argument was that gene duplication allowed for that gene to lose part of its function. Then, when the original gene lost its promoter region function through a mutation within that region, then the new phenotype emerged.
So, it’s gene duplication at the service of ‘gene loss.’ No information is added, and then some is lost. And, overall, speciation occurs when this happens. Who would have thought? (Hope you’re paying attention wd400)
PaV – wrt novel genes, once more google is your friend. Again, first page of results.
You’re still punting the problem of gene loss/gain, so I guess we’re done there. And I still haven’t seen any maths from you about overcoming long odds, so I guess we’re done there too.
The ‘genetic diversity’ argument doesn’t work wrt bacteria:
Andreas Wagner:
Besides the obvious problem for Darwinian theory that sexual reproduction is far less efficient than asexual reproduction, there is also the burning question, on the Darwinian perspective of ‘survival of the fittest’, of why bacteria don’t eat us.
If evolution by natural selection were actually the truth about how all life came to be on Earth then the only ‘life’ that should be around would be extremely small organisms with the highest replication rate, and with the most ‘mutational firepower’, since only they, since they greatly outclass multi-cellular organism in terms of ‘reproductive success’ and ‘mutational firepower’, would be fittest to survive in the dog eat dog world where blind pitiless evolution ruled and only the fittest are allowed to survive. The logic of this is nicely summed up here in this Richard Dawkins video::
In other words, since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but efficient reproduction be realistically ‘selected’ for? Any other function besides efficient reproduction, such as much slower sexual reproduction, sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of efficient reproduction, and should, on a Darwinian view, be discarded, and/or ‘eaten’, by bacteria, as so much excess baggage since it would slow down efficient reproduction.
Humorously, the real world example that Dawkins gave to Dembski, (in Dembski’s critique of the hidden teleology within Dawkin’s “WEASEL” program), illustrates exactly this point, i.e. the point that natural selection can only ‘see’ efficient reproduction and will ‘discard’ any excess baggage:
Yet when we look at ‘Spiegelman’s minivariant’ we find:
Needless to say, Dawkins real world example of ‘Spiegelman’s minivariant’, i.e. loss of information to gain a reproductive advantage, to support his WEASEL program to Dembski is NOT what Dawkins needed to prove his point. But in actuality Dawkins’ real world example proved Dembski’s ‘hidden teleology’ critique of Dawkins’ WEASEL to be right on the mark and also shows that ‘survival of the fittest’ is primarily concerned with efficient reproduction and nothing else.
Moreover, contrary to this central ‘survival of the fittest’ assumption of Darwinian evolution, instead of eating us, time after time we find micro-organisms helping each other, and us, in ways that have nothing to with their own ‘survival of the fittest’’ concerns. The following researchers said they were ‘banging our heads against the wall’ by the contradictory findings to Darwinian theory that they had found:
Moreover, instead of eating us, as would be expected an a Darwinian view, time after time different types of microbial life are found to be helping us in essential ways,,,
Moreover, there is very good reason to believe that pathogens were benign for most of their history and only recently became pathogenic
Moreover, contrary to Darwinian thought, there is also good reason to believe that many pathogenic viruses and bacteria are caused by a loss of functional complexity not a gain.
For instance, a genetic study has shown that bubonic plague (Black Death) was caused by loss of genes and streamlining (genetic entropy) of a non-pathogenic bacteria:
Frankly, it is very good that there is a strict limit to what evolution can create, (Behe: 2 protein/protein binding site limit; Edge of Evolution), since it allows us to develop drug treatments that are beyond the capacity of Darwinian processes to overcome:
The multiple drug cocktail that has been so effective in controlling HIV uses much the same strategy of being beyond the ‘edge of evolution’ that Dr. Behe has elucidated:
And it is also very good that genetic entropy is true. Sanford has shown that the destructive effects of pathogens on humans are fairly quickly are modulated by information loss.
ba77 @93 –
But they do. Well, a few do.
‘But they do. Well, a few do.’
Take your dogma glasses off so you can read for comprehension for goodness sake. That concern was addressed.
We no longer say: “Another day; another bad day for Darwinism.” We now say: “Another day since the time Darwinism was disproved.” Love it!!!!
Bornagain77: Can’t thank you enough for all of your comments, not just in this thread but in all threads on this site. Great work!
TWSYF, can’t really take credit for it. I shamelessly steal from others on UD and use their insights! 🙂
rvb8 @88
Did you actually see me say anything like that? No, you didn’t. In fact, you have sadly failed to understand my point.
My point is actually the opposite of what you’ve suggested. My point is that because Darwinian evolution is held to be a purposeless process lacking in any goals, evolutionary explanations for why some biological feature evolved are typically empty and misleading, because there is no reason that any biological feature evolved. There are only possible reasons why already evolved, functional features might be selected for.
The thing is, in my experience, most casual believers in evolution ultimately think of evolution as a purposeful process. They think this because 1) they are constantly given teleological explanations for why biological features evolved (e.g. Feature A evolved because it has benefit X), and 2) their common sense tells them that ‘just because’ is an insufficient explanation for how a complex system could have arisen and been in a position to be selected for in the first place.
These kinds of teleological explanations are common among science popularizers as well. For example, Bill Nye, in his debate with Ken Ham a couple years ago, talked about this very issue of the evolution of sexual reproduction. He started off by saying how it initially made no sense to scientists, because it was so inefficient when compared to asexual reproduction (there’s a joke in there somewhere), but then they realized that it offered the chance at greater genetic diversity and could help in coping with disease. Because of this potential benefit, Bill Nye then said that sexual reproduction was a fulfilled prediction of evolution.
Of course, Nye clearly didn’t mean that sexual reproduction is a prediction of evolutionary theory in any specific sense. What Nye was saying was simply that evolution predicts that advantageous things will evolve. But this isn’t true. Evolution doesn’t predict that advantageous things will evolve. It predicts that, assuming all other things are equal, already evolved features will be selected if they are advantageous with respect to increased survival and reproduction. Explanations for the selection of features are not the same thing as explanations for the evolution of those features in the first place.
Teleological explanations for the evolution of biological features are a blatant cheat, but they are used because they help sell the plausibility of evolutionary theory to the public. Noting that some feature confers a particular benefit is a perfectly reasonable explanation for why something would have been designed. It is not a reasonable explanation for why it would have been initially produced by a purposeless process that didn’t have the benefit in view or the feature as a goal.
Um, an ID question would be identical, but would not simply assume that the feature exists in humans solely because it was inherited from some ancient ancestor and served no particular purpose in humans themselves. ID would also offer teleological answers that are not strictly confined to issues of reproductive fitness. And teleological answers under ID could actually serve as legitimate explanations for why some feature might have been designed and implemented, rather than simply selected for after it has managed to arrive on the scene through a series of happy accidents.
This statement from rvb8 sums up the whole debate nicely:
“It seems that everyone here is hell bent on asking, ‘then why are we here, why are we so special?’ If this is your question, then it sadly fails to understand Darwinian Evolution. We reproduce sexually because we inherited this method from ancient ancestors. The ligitimate question of why we went down this evolutionarily less efficient method, is what science is trying to answer.”
In other words, Darwinian evolution has become truly an unquestionable religion. It has come to the point of being able to substitute the word “God” for evolution and it would not read any differently.
Of course if we are good scientists we must question why something happens. Any scientific theory must hold up to all challenges. So if we cannot explain humans through RM&NS then those mechanisms are falsified for our existence and the whole theory fails.
Yet we are told we reproduce sexually because we had ancestors who did. It’s all an a priori assumption. Do not dare question the sacred evolutionary tale! Prove how our ancestors developed sexual reproduction and prove we actually could arise through chance from those ancestors. I was never asking why humans reproduce sexually, I was asking why any organism came about from an asexual ancestor through accident to reproduce sexually, it makes no sense by the definition of what evolution is about.
Bob O’H:
Couple of problems, Bob: first, what they consider to be “novel” genes, are really “de novo” genes. Second, which confirms the first point, here’s what they say:
So, what has really “evolved” since 50 million years ago? Not much, and mostly mammals. And they study flies mostly.
Sorry, this doesn’t help your cause.
Duplicating a gene is not a gene “gain.” They have genomic sequence data that demonstrates–not just theorizes–that what differentiates species is the “loss” of genes. You’ll just have to learn to live with it.
As to the maths, it is you who must provide the recipe for overcoming long odds, not me. I still await.
To simply grandstand and say “evolution” happened, and therefore long odds were overcome, is to simply put the cart before the horse. This is convincing to no one.
PaV – you’re clearly not using “de novo” and “novel” in the way they are used in the literature to describe genes, so can you explain what you mean by these terms please.
Bob:
I’m now wondering if there is equivocation going on within the literature itself.
In the article I’ve cited, “novel” means that there is no connection to annotated sequences. To me this means that the gene is entirely new. It the paper you cited, the two terms seemed to be used in the opposite sense.
So, to me, I’m using “novel” to mean that it is a gene that has no connection to already known, and annotated, sequences, and so cannot represent a product of duplication and degradation, or inversion.
Bob:
Let me add that the way “de novo” is used in the literature amounts to equivocation. “De novo” means, more or less, something that is utterly new. When you have a piece from here, and a backwards piece from over there, that’s not “de novo.”
It only helps to obfuscate things.
Here, for example, is the very first sentence of an abstract from April of last year:
This sloppiness is unfortunately not uncommon in evolutionary literature.
Of related note to ORFan genes.
Alternative splicing is very different between species. Even very different between chimps and humans:
Moreover, alternative splicing allows for the same gene to code for multiple different protein products:
Moreover, “Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes.”
Thus, since alternative splicing is very different between different species, even very different between chimps and humans, and since alternative splicing produces up to a million polypeptides that appear “as if encoded by distinct genes rather than as minor variants of each other”, then it is very reasonable to conclude that the “ORFan gene problem” is actually far more problematic than Darwinists pretend that it is.
Supplemental notes:
Alternative splicing is a very big part of what we’re discussing here, and yet it doesn’t seem to factor into the notion of “de novo” gene.
Thanks for the citations.
Has anybody read vjtorley’s June 6th “Consider the opossum: the evidence for common descent” thread? Apparently all of us mammals have lost our genes for making egg yolks. Are we thus doomed?
Hello, bornagain77,
Thank you for your posts. You routinely expose the mere sophistry at the core of the doctrines promulgated by the apostles of the Church of Darwin and demonstrate that what has been masquerading as science for so long is in actuality only irrational, blind-faith-based atheism.
HeKS, “The thing is, in my experience, most casual believers in evolution ultimately think of evolution as a purposeful process.”
No! “You couldn’t be more wrong”, if you tried. Firstly we don’t “believe” in evolution, we accept it, for the robust science it is. Secondly, how do you ‘casually’ believe something, I don’t even ‘casually’ accept evolution, I rigorously accept it. Finally ‘teleology’ is a strictly religious dogma, it has no place in, inferred from the evidence, or observational science.
The whole of this post by HeKS which slurs science with religious sentamentalism is quite outrageous. We do not accept the supernatural because we can’t test for that. We do not accept a hiarchy of life because there is no evidence change has stopped, and we don’t know what will come next. We do make predictions (Tiktalik etc) and we do observe and test.
For years I have been reading this site, since your Waterloo, and I have yet to hear of any science comming out of Anne Gauger’s lab. Please stop insulting scientists with teleological motives, they don’t have them, that’s your sphere.
Heh:) You mentioed Ken Ham on a ‘science’ web site, good luck with that referrance to science:)
Yes, thank you bornagain77. You post a lot of great links.
Incidentally, I made my “Darwexit” in college as a result of studying biochemical reactions.
-Q
rvb8,
Do you actually read what people say or are you just a troll?
Yes, I mentioned Ken Ham’s name to give you context for where Bill Nye made the comments I was referring to. What’s your point? I wasn’t citing Ham for anything and wouldn’t, since I’m not a YEC.
As for teleology, there is nothing inherently religious in the word. You don’t seem to have the slightest clue what you’re talking about.
People regularly offer teleological explanations for why things evolved, which is a practice that is in fundamental conflict with evolutionary theory. What don’t you understand about this?
And what is a ‘casual believer’ in evolution? Someone who accepts it because they’ve been told it’s true but has never actually bothered to understand the theory, the evidence that is cited in its favor, or the evidence that is cited against it. Most people have a very poor understanding of any and all parts of the theory. They believe it because they were told it was true in school and they never really cared to question that one way or the other.
Your comment is full of bluster and even more nonsense. You didn’t bother to seriously address any of the things I actually said, so why are you bothering to direct comments to me? Go troll someone else.
PaV – I don’t think it’s equivocation, more that most geneticists use ‘de novo‘ and ‘novel’ in different ways to the way you are using them. But if you want references to the way novel genes (in your terminology) come about, read the papers I linked to @80.
FWIW, the paper (I assume you mean the one cited in the OP) doesn’t use de novo to reference gene origin, and the only relevant use of ‘novel’ is in a sentence about “novel ‘patchy’ orthologues that reveal previously hidden origins of ancestral gene families”, so clearly it doesn’t mean ” that there is no connection to annotated sequences”.
For me, a ‘novel’ gene would (probably) mean one with a novel function. But YMMV, depending on context.
as yo:
“Please stop insulting scientists with teleological motives, they don’t have them, that’s your sphere.”
UMM no, they do have them regardless of whether they admit to them or not
Of related note:
This working biologist agrees:
as well:
rvb8 @ 110:
“We do not accept the supernatural because we can’t test for that.”
Please describe how one would test the hypothesis that all that exists is natural.
Doh!
Bob O’H:
It is now common for articles to say that “de novo” genes come from non-coding DNA. This is simply a way of saying that it comes from DNA that is not annotated since translation of the DNA would produce amino acid products that would likely have been annotated by now.
Having thought over the reality that “de novo” genes seem to come from NC DNA, coupled to the fact that scientists have a hard time wrapping their minds around how these “new” genes can be ‘functional,’ i.e., what happens that allows these new genes to incorporate themselves into the overall functioning of the cell/organism, it strikes me that the best explanation for this–and this comes from an ID perspective which looks at these types of dilemmas as an engineering type problem—would be that these “de novo” genes are simply ‘genes’ that have been stored away for future use; a kind of back-up ‘drive’ for the genome, and so, they have essential markings for insertion into existing cellular machinery, or, that transposons, e.g., provide the added needed machinery.
The whole idea of “frame shifts,” then, can possibly be viewed as a way of ‘storing’ this information in the DNA in a hidden manner: i.e., another layer of information storage.
However, if we can, at long last, get back to the seminal paper in this discussion, then if “de novo” genes are nothing but ‘un-hiding’ ‘hidden genes,’ then the “information” is already there, and the machinery of the cell simply ‘finds’ it. But, ‘gene loss’ involves a complete loss of information in many cases, and, we’re told, this leads to speciation.
What is obvious here is that this is the complete opposite of the Darwinian/neo-Darwinian narrative.
OTOH, this fits in quite nicely with the ID conception of “front-loading,” a concept that has been talked about for twenty years.
The war is over: we won!
@Alicia #71
‘let’s say take the number of things we have at least a partial explanation for in evolutionary biology, now take 1% of that, and that’s the number of things that if we had absolutely no explanation for or completely went against everything we know, then I would begin to question evolution.’
‘… at least a partial explanation…’?
But that is like the children’s game of pinning the tail on the donkey, isn’t it ? Groping about in the dark, blindfolded, looking to establish coherence and intelligibility. You know, it just takes a single false assumption to end up in Bedlam, as the economist J M Keynes put it, in a review of one of Hayek’s ‘oeuvres’.
However, when each fork in the road can lead closer and closer to the madhouse… it’s really not good – no less in science than in theology or any other discipline.
Just as an update, it really shouldn’t be (at least for the time-being) a “we won”; it should be “James Shapiro’s NGE” has won.
PaV – yes, getting back to the original paper, how important is gene loss in evolution, as compared to (say) gene gain? I don’t think any evolutionary biologist would object to the idea that genes can be lost. But it could only rarely be important, or (speculatively) the function of the gene could have been taken over by another gene, in which case this doesn’t do much to support your case. So, you’re going to have to do more before declaring victory. After all, you can’t declare victory in a war just because you killed one of the enemy.
Incidentally, as you’ve brought up front-loading, how does front-loading theory view genetic entropy?
Bob O’H:
Front-loading and genetic entropy are hand-and-glove. Unless there is “front-loading,” the genome cannot afford entropy (loss of information).
PaV – but genetic entropy degrades genetic information. So how are front-loaded genes prevented from being degraded?
Bob:
If one is willing to look at things intuitively, one will see that we’re moving in the direction of greater and greater gene processing capacities. wd400 consistently takes the position that everything a cell does, it does because of what is contained in the genome. IOW, it’s all coded in. But the problem with this position, of course, is that there are no intermediates between rocks and bacteria, nor between prokaryotes and eukaryotes. So, then, if all of this functioning is simply part and parcel of what cells do, then how did this process come about? Where did all the DNA genes and RNA genes come from? What gave rise to them?
There are no answers to these questions. And then there’s the Cambrian explosion.
This is all ground we’ve covered before; but, it tells me that sooner, rather than later, biology will be forced, little-by-little, the more far-reaching theses of Darwinism. In fact, as we know, this process is now taking place with the MS being reevaluated.
Intuition, seeing and penetrating the essence of realities more powerfully than simple logic, should suggest, even now, that Darwinism is a failed attempt at explaining biological origins. (Even plain and simple “adaptation” looks to be the work of the inner resources cells possess)
The handwriting is on the wall, so to speak.
I can’t help but think of the time I was in a library and opened a reference book on the history of science. The most remarkable revelation was concerning the shift from the Ptolemaic view to that of Copernicus: the so-called “Copernican Revolution.”
Well, this “revolution” took right around 100 years. You have to admit, that was some kind of ‘slow’ revolution!
I hope the shift away from Darwinism happens a little bit faster.
Bob O’H:
Front-loaded genes are NOT prevented from becoming degraded. And “speciation” would be the result of this ‘degradation.’ You see why this fits in so well with the paper cited in the OP.
This view—per Denton, a’one-time’ front-loading brought about completely by the ‘nature’ of the natural order—requires that each of the major “explosions” of forms (including the mammalian explosion) a kind of infusion of information would take place. From there, information decreases, and species increase.
PaV – but if front-loaded genes are being degraded, how come they are still functional? Or are only some functional when they are needed?
I don’t see how you can have it both ways – genes laying around inactive, and genetic entropy happening, but then when these genes are needed, they are fully functional. I assume I’m missing something here, so it might help if you fleshed out your model more fully. Intuition is great, but it’s only a starting point.
(and having asked you to flesh out your theory, I have to apologise in advance if I don’t reply after this evening – I’m off to Seattle for a conference).
Hi Bob
I made the cell phone analogy to demonstrate how unlikely adding information to a sequence is. It turns out that an op on our discussion was written at the skeptical zone. Sequences ( phone numbers, the english language, DNA, Proteins) are great for creating diversity but they break down with random change. Evolutionary biologists like Michael Lynch have tried to model adaptions mathematically and the results have been long times and large populations with adaptions requiring only a few changes. This is because the genome is a sequence.
Bob:
Genetic entropy, as it is presented by John Sanford, has more to do with degradation of information in general. That would be the general model. NS would be seen as part of the correction process. Fred Hoyle concluded as much.
However, the kind of genetic entropy I’m referring to would involve speciation events associated with the continual loss of gene function, and even the loss of genes themselves. But this is more peripheral to the ID perspective. (More on that later.)
Gene-centric Darwinism, OTOH, would see gradual gene gain.
Any notion we have of gene loss/gain is glimpsed only through comparison of the whole genome of related organisms. That’s essentially all we have to look at. Per “front-loading” in the “gene-centric” sense, the more basal organism would be the one which has the least amount of loss. That’s about as much as you can say.
However, the ID perspective has always understood ‘genes’ as simply the building blocks of organisms, with the blueprint of construction being located somewhere else in the genome—what has been, until now, called non-coding DNA, or, even, “junk-DNA,” and representing the much more important and essential part of what an organism is.
Thus, as techniques for faithful sequencing of the ncDNA improve, and they too become “annotated,” then the blueprint of major taxonomic lineages should emerge as the ncDNA is better understood and begins to be correlated with taxonomic groupings.
So, when ID talks about “front-loading,” it’s not the traditional notion of the gene, per se, that it has in mind. Take, for example, transposons. These little creatures move about in the cell with their powerful machinery. It is entirely possible that they involve, and then un-involve, various gene products as the organisms adapts to its environment. A recent paper has shown that inbred populations that have adopted to their environment show clusters of transposons that have built up. So, transposons, would be something more central to the ID perspective, with the interesting question becoming: what is directing the movement of these transposons. It’s not the genes they activate that is of interest, but the actual genetic machinery at play: what’s driving all of this.
Yet, even here, this is something more tangential to the more essential view of ID. Our focus would be on the discovery and understanding of basic embryological developmental programs. These ‘programs’ would involve, very likely, ncDNA. Recent studies, e.g., have shown that “pseudo-genes” are very much involved with the development of the brain; what once was considered “junk-DNA”, or ncDNA, seems to play an important role in developoment and speciation. Will this trend continue?
Assuming it continues, ID predicts discontinuity of these eventually discovered ncDNA ‘programs’ between major lineages. NS, and mating, would correct the genetic entropy involved in these programs, and so we should find a high degree of conservation. These would be some basic expectations.
Meanwhile, the importance of gene ‘loss’–what we’ve been discussing here—is that it paints a picture of genomic inheritance showing growth in species via “information” loss.
The ‘build-up’ of bau-plans for the major lineages then becomes very hard to support, and any discovered discontinuity of these plans would require invocation of some other effective agency.
To me, that’s where science will likely lead, a kind of ‘end-point.’ And then everyone will be free to understand it any way they like. But, neo-Darwinism will have be shown to have failed as an explanation.
I’m opposed to Darwnism, not so much because of its anti-religious implications, but because it is simply bad science.
Based on what I’ve seen so far, and especially within the last few years, I’m certainly ready to write its obituary. Perhaps I already have.
Have a nice conference. Meanwhile, the work of many scientists in the lab leads us forward.
PaV
I completely agree with you here. The problem is when this theory unwinds to causes that can be tested, what is left? Do we tell everyone we were just kidding there is no theory of evolution? The gap that has formed between real testable science and public perception is enormous.
PaV @126
I once accepted theistic evolution, thinking that God’s perfect providence might have arranged for natural selection acting on predestined variations or mutations could have resulted in life as we find it now.
But after following the debate for years I ended up where you are: Darwinism is simply bad science.
And it also became clear to me that the notion that inanimate matter somehow mindlessly and accidentally assembled itself into self-replicating, digital information-based nanotechnology the functional complexity of which is light years beyond our own was simply batsh*t crazy.
Harry
Exactly, I would not be surprised if neo darwinian theory goes down in history as the worst scientific idea anyone has ever had.
Harry, Bill
I once thought that the general state of humanity is one of sanity interrupted by short flashes of delirium. Nowadays I hold the opposite view.
////the notion that inanimate matter somehow mindlessly and accidentally assembled itself into self-replicating, digital information-based nanotechnology the functional complexity of which is light years beyond our own was simply batsh*t crazy.////
This statement only shows your ignorance and laziness.
Inanimate matter did not somehow mindlessly assemble into living things. That happened via distinct processes and our challenge is to understand those processes. Instead, what you and your ilk are doing is to resign from the hard work and attribute everything to an imaginary designer for which absolutely no evidence exists.
“I don’t understand and I cannot imagine how something came about. Therefore God must have done it.” <<< That's your position. But it doesn't work, I'm sorry.
The Origin of Life: An Inside Story – March 2016 Lecture with James Tour
https://www.youtube.com/watch?v=_zQXgJ-dXM4
Origin of Life: Professor James Tour – May 1, 2016
Excerpt: “All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated…
So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal.
You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.“
James Tour – leading Chemist
http://www.uncommondescent.com.....nt-design/
I’m rolling on the floor laughing seeing Pav’s unilateral declaration of victory. What nonsense is that fellow blurting out?
Gene gain and gene loss are all part of evolution, that’s neither anything new nor beyond the capability of standard evolutionary processes. He talks about frontloading? Mammals evolved from reptiles, who evolved from amphibians, who in turn evolved from fish, which evolved from invertebrates. And there have been multiple events of gene gain and loss all throughout these transitions. Where exactly is the frontloading?
His statements on de novo genes are nothing more than shifting goalposts. First he claims de novo genes spring out of nowhere hinting that his imaginary designer introduced them. Then when someone pointed out that de novo genes arise from noncoding DNA, he does the classic creationist trick of shifting goalposts. He then starts claiming de novo genes were “hidden” in the genome waiting for the right moment when the designer felt that they were needed.
Pav’s designer can have it anyways, he’s ultra-flexible. That’s because the deisgner is not only imaginary for which no evidence exists, but also one whose properties, capabilities, limitations and intentions are all unknown. Therefore creationists can spin any scenario to fit their designer! And no one can question it!
By the way, here’s a good recent review on de novo genes:
http://www.cell.com/trends/gen.....0034-7.pdf
They arise when mutations in non-coding DNA introduce binding sites for transcription factors or remove stop codons or join short protogene products into a larger gene. None of these are beyond already known processes and, as such, does not require invoking a designer for explanation – except for creationists.
Evolve @ 131:
But according to the theory you support, it did exactly that. Why do you feel the need to deny that?
No, I already mentioned above that distinct processes were involved, not aimless, mindless assembling as creationists always claim. If we can figure those processes out, we’ll solve the problem. What’s needed is the resolve and commitment, the hard work and dedication to probe the unknown. The creationist attitude of resigning to the easiest answer will take us nowhere. It’s a dead end.
Denying the law of biogenesis, i.e. that life always comes from life, is unscientific and is more of a ‘dead end’ than you can possibly imagine right now:
If we can just figure out how these teleological processes work we’ll be able to rule out teleology!
BA77:
More accurately, physical annimate life has only ever been observed coming from other physical animate life containing similar genetic material. In that case, both a natural cause of the origin of life and a supernatural cause suffer from the same weakness.
Evolve
Can you show any experimental evidence of the origin of a de novo gene? Mathematically sequences degrade with random change. How much time and how large of a population would it take to get a de novo gene of 5 required mutations?
Moreover, stubbornly refusing to accept the blatantly obvious fact that life is designed hampers scientific progress, such as was witnessed in the decades long junk DNA fiasco.
Whereas, honestly admitting that life is designed leads to scientific innovation.
Don’t believe me? Well, there is a new burgeoning field of Biomimetics that seeks to imitate the design found in life so as to foster innovation in man-made designs, since the design found in life is often times far, far, better than anything man has ever designed thus far.
Here’s one from as far back as 2009. It’s open access I think.
http://www.sciencedirect.com/s.....2209014754
They report the origin of a new gene in mouse from an intergenic region. This region is present in rats and even in humans! But, only in the mouse, has it acquired the mutations allowing it to be expressed as a gene.
In Figure 3, they show a phylogeny illustrating how functional mutations were acquired by various species tested. Humans are the outliers with 4/6 required mutations absent. Next come rats, in whom 2/6 required mutations are absent. Then comes various species of mice, who have either 1/6 required mutations absent or all required mutations present. Thus, even the phylogeny of this new gene matches the general phylogeny of humans, rats and mice!!
Trying to explain this data from a design perspective will be laborious and contrived (if Pav ever attempts to do that). For example, why would a designer insert this region into humans with 4/6 required mutations absent rendering it non-functional? Why would he insert the same region into rats with more functional sites but still 2/6 missing?
It makes no sense at all! Only an evolutionary explanation makes any sense here.
This is why no real scientist will be swayed by the kind of nonsensical victory declaration Pav is making. The data strongly supports evolution.
Hi Evolve
Your paper clearly states that it is difficult to infer the mechanisms of gene emergence. This is because the genome is a sequence. Random change rapidly breaks sequences down. Think about making random changes to the direct dial numbers in your cell phone. Will this find friends that are not currently in your direct dial? What it will do is get rid of numbers of people you don’t want to talk to any more. A successful adaption 🙂
Perhaps MC would like to explain this without reference to the supernatural?
There is fairly strong evidence that photosynthesis goes all the way back to the first life:
Yet photosynthesis is dependent on quantum coherence for photon transfer
To be clear, quantum coherence, like quantum entanglement, is a ‘non-local’, beyond space and time, effect
As a Theist, I have a beyond space and time cause to appeal to explain non-local photosynthesis, whereas the materialist has none to appeal to.
Hi Art
If I duplicate a phone number in the direct dial of my cell phone have I added information? Perhaps, but I have not added a new contact which would indeed be new information.
Evolve @141:
Let’s take a step back a second. Like most naturalists, there is a clear misinterpretation of what I consider to be the standard model that most ID proponents take. You, like others, fall into the trap of believing that anyone who supports ID or does not subscribe to naturalistic evolution is a purist and simplistic creationist. This is a complete fallacy and a misunderstanding of the common position (I hasten to add, even one held by most YECs).
It is not black and white, it is not evolution or no evolution at all. I think PaV has been demonstrating this the whole thread here. Most IDers fully accept that evolution of sorts does occur. What is contested is to ability to direct molecules to man or create new meaningful information from no information. That is the whole point of this thread. Do you really think even YECs would say that God created antibiotic resistant bacteria? Of course not – microevolution is a fully embraced phenomenon but that is selection acting on existing information.
So with that in mind, on to your cited example of the pldi gene in mice. This is certainly an interesting case but there are a number of things that need to be studied further. Firstly, it is surprising how this is what you reference to support your case given how so many of the naturalists around here downplay the importance of lncRNAs. This does appear to be, by all means a non-protein coding sequence. That does in fact raise the question of the fact so many lncRNAs are being described these days, and outside the normal expected gene start consensus sequence sites, as to how much work has been performed to demonstrate that the region is not functional in humans or other species that lack these particular mutations described to give pldi it’s mouse specific initiation sites?
Secondly, why if this is not an important region in humans, does this portion of sequence appear to be under “purifying selection”? In this study:
The de novo sequence origin of two long non-coding genes from an inter-genic region
Yulin Dai et al
They state:
So why in the world would purifying selection occur on a sequence that has no function, pre “gene-birth”? What selective advantage is gained by having a non-functional region present that would mean less drift would occur in this region? How does RM+NS account for that observation?
Further, the authors state:
So there is perceived to be function in this region. What is that function? No one knows but the point is this is not a useless stretch of DNA that a gene popped into existence from.
So going back to my original point, and more pertinently PaV’s point, nothing here is inconsistent with a front loading event. In fact, quite the opposite. Whilst this paper is interesting (and I’m sure not the first time you have brought this up), it is certainly not inconsistent with what is being discussed in this thread.
Personally, I suspect this is much more complex than we realise. I also think that you can look at things the other way around – genetic loss in a number of organisms (weak spots, susceptible to viral endomucleases and other similar phenomenon). Emergence of sequence is one explanation but disappearance is another to consider (except it is ruled out as it does not fir within the naturalistic evolutionary paradigm). I am not saying this has occurred here,but it is worth considering in general.
BA77:
Here, I fixed that for you:
That would certainly explain why all of the scientists studying quantum physics are theists.
Correct me if I am mistaken, but are you now breaking the cardinal ID rule and proposing a mechanism for turning design into reality? That would certainly be something that could be researched and tested.
In what sense is inanimate matter “not aimless” and “not mindless”? Does inanimate matter have life in mind?
MC, redefining ‘natural’ to include beyond space-time matter-energy effects, is a disingenuous ploy. By your new definition of ‘natural’ the Big Bang itself is now itself to be classified a ‘natural’ event since it also cannot be explained by within space-time matter-energy events.
No less than Einstein himself considered non-local quantum entanglement to be ‘spooky action at a distance’, and sought a materialistic explanation to circumvent it:
Quantum Entanglement is simply completely incompatible with the reductive materialism that Darwinian evolution itself is built upon.
A few supplemental notes:
BA77:
Nobody is redefining “natural”. Quantum physics is just helping us better understand what “natural” is. Just as classical physics and chemistry did before that. With regard to the Big Bang, that question is still to be answered. But my money is on natural. Remember, natural doesn’t have to be common place. Which in some instances is a good thing for life on earth. If super novae, a natural occurrence, were far more common than they are, it is unlikely that life as we know it could get established.
And Newton believed in God. Even the most intelligent people are sometimes wrong.
magna charta,
“Nobody is redefining “natural”. Quantum physics is just helping us better understand what “natural” is.”
So the word ‘natural’ has a fluid definition that is subject to change whenever experimental outcomes conflict with the present definition of the word ‘natural’?
Well by golly, how could I have been so dense as to think you were disingenuously redefining the word ‘natural’ so as to prevent falsification of the naturalistic/materialistic worldview? Thanks for clearing that up. (snark off)
BA77:
No. But knowledge of a phenomenon previously ascribed to the supernatural can result in it being re-classified as natural. There are many things we consider natural today that were considered supernatural in the past. I would provide examples but you obviously are far more proficient at Google than I am.
I have often wondered that about you. 🙂
“But knowledge of a phenomenon previously ascribed to the supernatural can result in it being re-classified as natural”
But never the other way round?
Well by golly, that is some set up you got there.
Of course others not so enamored with your one sided redefinition of natural to include beyond space-time matter-energy events might suggest the game is rigged towards ‘naturalism’.
Question, in your scheme of naming all experimental outcomes as ‘natural’, could God himself someday be classified as ‘natural’ in your scheme of redefining all beyond space-time matter-energy things as ‘natural’? If not why not?
as to:
” There are many things we consider natural today that were considered supernatural in the past.”
do you think of a atom as ‘natural’?
BA77:
I don’t see why not.
First, we don’t know that entanglement is beyond space time matter energy things. but that is beside the point. The God you believe in wouldn’t be considered natural. Because, as far as I know, it can’t be affected, other than by getting angry or happy, by any natural physical actions. However, i can’t speak for all gods.
Yes.
“First, we don’t know that entanglement is beyond space time matter energy things.”
Actually all experimental and mathematical evidence we currently have, some of which was already referenced, disconfirms any materialistic, within space-time matter-energy, interpretation of quantum entanglement
This is a well known scientific fact. For you to deny the current state of affairs in quantum mechanics reveals either a irrational bias against the implications, or a profound ignorance of the current state of quantum mechanics. Perhaps both.
As to you arbitrarily excluding God from your definition of the word natural, yet readily including ‘spooky’ quantum entanglement within you definition of natural, even though Einstein himself fought against quantum non-locality since it went against his naturalistic assumptions, reveals your irrational bias against God.
Moreover, I guess reality not existing until we look at it is also to be considered ‘natural’ in your forever flexible definition of the ‘word’ natural?
Of related note:
Perhaps you can forgive me MC when, if you continue to pester me with such irrational reasoning, I will ask the admin of UD to remove you for trollish behavior?
Verse:
BA77:
The point I was trying to make is that we only know about these effects by measuring physical parts of the universe. If these effects are caused by the physical parts, then they are not supernatural. If they are caused by the unknown and unknowable that is outside of time space matter energy, then it is supernatural. And we don’t know one way or the other.
If that is going to be your response to every difficult question that I ask you, maybe you should go ahead and do that. But all onlookers can readily see that I have not been trollish. But it is your call. I can live with whatever you decide and wish you well either way.
Bornagain noted:
No, because anything outside of our universe, especially what created our universe, is considered, by definition, supernatural.
For example, that’s why the multiverse is considered supernatural. No, wait. That would be natural too.
Ok, let’s try again.
Anything outside the universe that’s natural that could have caused our natural universe, is natural. Naturally.
And the difference between a hypothetical God making the Big Bang happen and Nature making the Big Bang happen naturally, is that Nature did it by accident!
We now know it was an accident because accidents are Natural and God is not natural, so it must have been Nature, which proves that God can’t exist because he didn’t to anything.
So, given an infinite amount of Time, you get an infinite amount of Chance. And an infinite amount Chance can result in anything or everything including the Space, (local) Time, Energy, and Mass of our universe.
So you see, bornagain77, it all makes sense to those who refuse to accept the evidence screaming in their face. 😉
-Q
So Q, are you basically saying that his explanation just ain’t natural?
🙂
magna charta:
Quantum mechanics helps us understand the physical world, yes; however, it also has an ‘underbelly’; viz, the Copenhagen interpretation, which is, itself, based on positivist thinking, a brand of philosophy.
Entanglement, and with it non-locality, something first pointed to by Schrodinger, ( no fan of the Copenhagen Interpretation) is not well understood. The ultimate foundation of entanglement could wind up having a seemingly supernatural cause.
But here’s the problem: if we search “matter” for answers, we may, or may not, get them. If we search our “minds” for answers, again, we may, or may not get the answers. Yet, to perceive that something is an “answer,” itself requires the functioning of the ‘mind.’ So, it all boils down to this: what is the origin of the mind?
Is the mind completely “natural”? Does QM describe it?
How would you answer these types of questions?
Of note:
JDD,
///Like most naturalists, there is a clear misinterpretation of what I consider to be the standard model that most ID proponents take.///
Not right. Although short on time, I follow creationist literature whenever I get a chance and so I’m very familiar with your false claim that microevolution can happen, but macroevolution cannot. This has been debunked ad infinitum. If microevolution can happen, then no barriers exist to prevent macroevolutionary change. I can do no better than what TalkOrigins has said on the subject years ago:
http://www.talkorigins.org/indexcc/CB/CB902.html
///What is contested is ability to direct molecules to man or create new meaningful information from no information///
Another typical creationist catchphrase: “molecules into man”!
No, molecules did not turn into man one fine morning as you imply. Molecules did not randomly assemble, either, just as mountains were not produced by random piling up of rocks and rubble. Distinct geological processes produced mountains. Likewise, distinct biochemical processes produced life as well.
It took hundreds of millions of years (not overnight) for the first life to emerge, which alone shows the rarity of the event.
And then there was an even longer, much more arduous journey to get anywhere close to man. This too involved myriad chemical and biological processes.
By the way, nobody intended to create man in the first place.
And nobody intended to create meaningful information either. You’re caught up in this perpetual teleological thinking: Somebody wanted to create living things, so he made information for it. Much like how somebody wanted to create a computer, so he wrote software for it.
But this kind of reasoning is unwarranted. Computer software can neither come about by itself nor chemically interact. On the other hand, a random sequence of nucleotides coming about by chance can turn into a gene if it can successfully interact with its surrounding molecules. That’s all that’s needed. Life is just a cascade of chemical reactions at the fundamental level. With a mutation here or there, the DNA strand can now maybe interact more strongly with more molecules. Then the reactions are much more efficient and it gets selected for naturally.
What we call “information” in life for convenience is nothing like man-made information. Life’s “information” actually is just a 3D molecular structure that engages efficiently in one or more chemical interactions. For example, the TATA Box is a DNA sequence to which transcription factors bind, facilitating the decoding of a gene. Why does the TATA box recruit transcription factors? The T-A-T-A bases impart a specific 3D structure that makes interaction with proteins easier. Molecular Biologists can fiddle around with bases to make such interactions weaker or stronger, thereby altering gene expression entirely.
///so many of the naturalists around here downplay the importance of lncRNAs///
No naturalist who knows what he’s talking about will downplay lncRNAs or any non-coding RNAs for that matter. They’re all important. However, creationists tend to over-hype such RNAs produced from non-protein coding regions of the genome. The reason is obvious, they want to prove that Junk DNA does not exist. But even if you take all non-coding RNAs discovered till date and liberally allow for hundreds, or even thousands, more to be discovered in the future, that still won’t invalidate Junk DNA! Because all those functional RNAs will still only constitute a fraction of the genome.
Evolve claims:
Here is a detailed refutation, by Casey Luskin, to TalkOrigins severely misleading site on the claimed evidence for observed macro-evolution (speciation);
Evolve then claimed:
And yet, despite the fact that nobody has a clue how Life can possibly originate naturalisticly (James Tour; An Inside Story – 2016), we have evidence of life suddenly appearing on Earth immediately following the late heavy bombardment
Evolve then claims:
And yet
Evolve then claims:
And yet,
Evolve then claims:
And yet, the chances of a protein developing a new protein/protein binding site so as to ‘interact with its surrounding molecules’ is 1 in 10^20 (Behe; White).
Evolve then claims:
And yet:
Evolve claims:
Apparently hardcore Darwinian biologists have no clue what they are talking about since they still vehemently defend junk DNA:
How about an experiment that even evolutionists can do if they don’t chicken out?
Take some non-motile bacteria in an environment favoring motility and expose them to massive quantities of ionizing radiation through enough generations to simulate millions of years of evolution.
If the bacteria are able to evolve cilia, flagella, propellers, or jet engines, you will have provided direct evidence. You will win the argument and become rich and famous!!
And if they don’t evolve . . . 😮
-Q
As to Behe’s ‘observed’ 1 in 10^20 ‘Edge of Evolution’
This finding is far more problematic than many people realize. Although many people have been misled to believe that Chimps and Humans are virtually identical, due to genetic similarity alone, yet due to alternative splicing, the protein-protein interaction profiles are vastly different between chimps and humans
Thus since alternatively splicing is very different between even humans and chimps, and alternative splicing produces proteins that behave as if encoded by distinct genes rather than as minor variants of each other and alternative splicing also produces strikingly different interaction profiles for proteins, and yet the ‘observed’ Edge of Evolution for Darwinian processes to generate a new protein/protein binding site are only 1 in 10^20, then we are more than justified to conclude that humans did not evolve from apes.
In fact, since humans possess a distinct alternative splicing code, we are more than justified to believe that humans were created distinctly:
An easy way of understanding why a unique code, such as the unique alternative splicing code that humans have, will never evolve in a gradual bottom up Darwinian fashion is elucidated by Dawkins himself:
In other words, a unique and new code, since the entire context of the code matters, must be implemented ‘top down’, all at once, in order to avoid ‘catastrophic effects’
Hi Evolve
This statement tells me you don’t understand how many ways a sequence of nucleotides can be arranged, for an average protein coding gene for just exons 4^1500. This number is larger than all the matter in the universe measured in atoms. There is no experimental evidence that more than a few adaptions have occurred in nature. This is due to the almost infinite ways to arrange nucleotides.
Of semi related note:
To- evolution scientists. Dear ladies and gentlemen. I am not a scientists like you but I can understand the fundamental aspect of science. there are four fallacies in yur conception of evolution.
Firstly. Darwin’s theory of evolution speaks about macro evolution and yu are speaking about micro evolution in other words some small changes within the species. Just like there are different varieties of dogs. There may be small or big dogs with different colors still they are dogs and are limited to its particular size.
Secondly- mutation in literal sense means changes or modifications and you people say such changes happens by various adaptive pressures and nature selects the protein and arranges in its particular sequence. Here Darwin himself has confessed that nature does not works randomly rather it “Selects”. This means that Darwin himself cannot explain the diversification of species without the idea of intelligent design or Selector.
Thirdly, you did not answer how the first self replicating cell came in to existence from inorganic matter by gradual steps of changes from a prebiotic soup.
Fourthly, DNA, RNA, Proteins and amino acids are all organic “Matter”. This means that it is just like an inorganic “Matter” like a thousands of spare parts of a car. Which themselves has no intelligence or energy to precisely assemble itself to make up a suffisticated car.
You people speak about a species gets adapted to such environment or circumstances and passes on its higher traits to its off springs. Here there is common misunderstanding. A species which lives in antartic ocean like polar bear or penguin when migrated to tropical countries cannot survive the hot climatic conditions rather it dies quickly before it gets adapted to that environment and passes on its higher traits to its offsprings. Even assuming that evolution from simple to complex forms to happen in randomness there must be Constant Favorable conditions for a positive multiple mutations and any unfavorable conditions will result in the destruction of positive mutations quickly. And life from simple forms to complex forms from single cell to humans becomes highly impossible. . as per the second laws of thermo dynamics such random energy destroys the molecules quickly and does not creates.