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New mechanism of evolution — POOF

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Each species has large numbers of unique genes that seem to have magically arisen without any ancestor. Evolutionists are saying they essentially POOFed into existence. These genes are referred to as ORFans or orphan genes. From the Max Plank Institute:

However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes
Evolutionary Origin of Orphan Genes

20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well. They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:

Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

😯

The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”

Experiments actually refute such assertions, but that won’t stop evolutionists from promoting demonstrably false ideas as some new discovery! And it’s not only the genes but the regulatory mechanisms that poof into existence:

On the other hand, there is now little doubt that new genes have arisen throughout the phylogenetic history and the general model of de novo evolution of genes appears to be well supported by now. However, this also raises several new questions. The foremost one is the question of how new promotors with a defined regulation can arise.

“de novo evolution of genes” is also another euphemism for the POOF mechanism.

But it’s not just the genes and regulatory regions, but also developmental mechanisms that deploy these novelties to create radical new species (like multicellular ones from single cellular ones).

gene lists can be associated with major evolutionary steps, such as the origin of germ layers, or the origin of multicellularity . Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes

Not only do the orphan genes emerge, they emerge with the most infrastructure to integrate them into the POOFED species. So genes, proteins, and developmental mechanisms, and new species also POOFED into existence. They sound almost like closet creationists!

The evolutionists conclude, evolution can do far more than we ever supposed because evolution can POOF thousands of genes and regulatory mechanisms into sudden existence rather than through slight successive modifications of an ancestor. What a wonderful discovery. 🙄

NOTES

1. Behe, who accepts common descent, is said to have jokingly used the phrase, “puff of smoke” to describe the mechanism that can create irreducible complexity. In internet debates, the phrase got converted to “POOF” to emphasize the magical character of the mechanism. It seems now, evolutionary biologists are seriously resorting to Behe’s POOF mechanism whether they want to admit it or not.

How did Behe arrived at the POOF mechanism which evolutionary biologists are now only discovering?

I lectured at Hillsdale College as part of a week-long lecture series on the intelligent design debate. After Michael Behe’s lecture, some of us pressed him to explain exactly how the intelligent designer created the various “irreducibly complex” mechanisms that cannot–according to Behe–be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking, he finally answered: “A puff of smoke!”

Larry Arnhart
http://darwinianconservatism.blogspot.com/2006/09/has-anyone-seen-evolution.html

2. Orphan genes have made the Irreducible Complexity argument that much stronger.

Comments
Have they identified the proteins in the specific organisms that are coded by these genes
GREAT QUESTION! Not always, and to my utter amazement, we haven't even found the proteins for many of the genes we think aren't orphans! I found this out when I watch how gene numbers were revised on a daily basis and when Eric Lander mentioned in a paper we need to confirm Gene existence via protein detection! Complicating this is the huge number of protein isoforms (slightly modified proteins) that come from a few genes through alternative splicing and somatic variation. There are perhaps millions of these proteins coming from 20,000 "gene" sites. What is disturbing is what we get in the popular press as fact and knowledge are actually educated guesses! We could be very different from chimps at the molecular level if the isoforms are different. We just don't know... Also, when I heard of immortal DNA, that means that DNA copies from cell to cell are slightly altered. This makes sense in a multicellular organism. How does that affect protein diversification. I don't know. Regarding immortal DNA: http://www.news-medical.net/news/2006/06/26/18558.aspx The discussion about Lander was here: https://uncommondescent.com/genetics/icc-2013-geneticist-jeff-tomkins-vs-evolutionary-biologist-who-got-laughed-off-stage/#comment-467843 I posted this discussion about orpahans as a precursor to reporting on Paul Nelson's keynote at ICC 2013 on Orphan genes. He's taken a lot of flak on the topic over the years, made a couple blunders (by his own admission) over the topic, but it looks like so far he is being vindicated. Apparently protein detection is really hard. I know enzymes can exist in 1 part per million. There are so many biomolecules in an organism, and it is hard to actually find them. Protein coding genes are inferred by the sequences, so there is a lot of work to do. Some of the retrogene (processed pseudogene) orphans were dismissed until we actually started seeing their products in the human body through cancer research. For all the embarrassments the YECs have caused for themselves over the years, the new generation of biologists in the YEC community are vindicating themselves and getting quietly published in secular peer reviewed journals. Tomkins is one of them, Sanford (obviously), others -- I've been asked to keep quiet on. :wink:scordova
August 16, 2013
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Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes
This sort of answers the question as to whether these genes are expressed but is not even close to a complete answer. If these genes are regulated let alone heavily regulated, they must be expressed somehow in some of the cells. What do they do? This is just one aspect of the evolution debate. But it is only a small part of the investigation into how complex novelties arose. Meyer's book begins the discussion about where the debate should be headed, embryo development.jerry
August 16, 2013
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@ 18 wd400 attempts to explain away the lack of ancestral lineage for ORFans. The lack of smooth transitions in the fossil record is also explained away as science claims the conditions for fossilization rarely occur. .... the empiricist sees no evolution.Johnnyfarmer
August 16, 2013
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These genes are referred to as ORFans or orphan genes.
There have been several threads describing these unique genes. Have they identified the proteins in the specific organisms that are coded by these genes and if so how they fit into the operation of the organism? It is nice that they exist but the real issues is just what they do.jerry
August 16, 2013
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Evolution takes functional proteins and tries minor variations. It does not randonmly assemble sequences from thin air.
No one disagrees with this but has anything but trivial changes ever occurred? This fact which you continually bring up is irrelevant to the debate.
Also nobody knows how rich in functional proteins the sequence space of all possible proteins is.
Apparently there are ways of estimating this. And it appears they are very rare. So rare that it is extremely unlikely that non-cocing sequences would turn into one. Maybe a few but not enough to make a difference. And then there is the issue of just how the organism would use the new coding section. Where are the instructions that put all the parts together and how would it fit in the new gene to develop new capabilities.jerry
August 16, 2013
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Is this the first use of "poof" on UD? https://uncommondescent.com/intelligent-design/rocky-mountain-news-reports-on-id/#comment-3427jerry
August 16, 2013
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'The de novo evolution model constitutes the largest conceptual step forward in our understanding of gene evolution.' Quoted from Salvatore's quote in his #16. 'A conceptual step forward...' Wow! these guys don't mess about incrementally, do they? Only modesty, presumably prompted their designation of their discovery of this great de novo poofery as 'a conceptual step forward', rather than 'a conceptual LEAP forward'. And Barry in his #25: 'Materialists love “poofery.” I’ve been pointing this out for years:' They have no choice, really, if they are to carry on with the motley, do they? Christ has the words of eternal life, but where else shall they go, since poofery has the words of eternal evolution?Axel
August 16, 2013
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Hi gpuccio I'm out and about and trying to enjoy the sunshine over the weekend but will respond fully when I can get to a proper keyboard. I strongly disagree on your superfamily claim. Have you seen Kirk Durstson's recent thread?Alan Fox
August 16, 2013
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#37 gpuccio
It is equally fair that ID scientists keep on seeking facts that support their theory, and explanations of how, when and why new information was inputted into living beings. That is, in making ID science.
Absolutely it would be fair if they did it. I am not aware of any attempt by any ID "scientist" to seek facts about how, when and why new "information" was inputted into living beings. Can you name one? Indeed how would they set about that task? (I put the quote marks round scientist and information because I don't want someone quote mining me to say I accept that ID is science and that information is something you can add like mass or energy.)Mark Frank
August 16, 2013
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Mark: It's perfectly fair that evolutionary scientists "keep on seeking explanations of how things poofed into existence", trying to give some kind of support to their hypothesis. It is not fair that they pretend to have explanations that they do not have. It is equally fair that ID scientists keep on seeking facts that support their theory, and explanations of how, when and why new information was inputted into living beings. That is, in making ID science. It is definitely not fair that you consider science only what is done under the dogmatic ideology of materialist reductionism.gpuccio
August 16, 2013
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Alan Fox: Coin tosses are absolutely relevant. Random variation is an essential part of the proposed neo darwinian algorithm, and coin tosses are the classic model for random events. Moreover, minor variations on existing functional proteins are not going to explain how new protein domains and superfamilies arise, which is exactly what we have to explain. Finally, while it is true that nobody knows exactly how rich in functional proteins the sequence space of all possible proteins is, it is equally true that we know much about that, and nothing of what we know is "darwinian friendly". I would say that the problem is that darwinists would like to keep that issue as dark as possible, because only that "ignorance" can give them an excuse to go on believing their irrational dogmas, while IDists are absolutely interested in clarifying as soon as possible the point beyond any possible doubt.gpuccio
August 16, 2013
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#33 gpuccio I think we more or less agree on the ID side. Given something that appears to "poof" it is sufficient explanation as far as you are concerned that a designer made it happen that way. There has been attempt of any significance to go beyond that - maybe a bit of informal conjecture about front-loading. The difference in our accounts is that I would say evolutionary scientists keep on seeking explanations of how things poofed into existence. You may not be satisfied with current explanations - that is beyond my skill to assess - but it is undeniably an area of continuing research with hypotheses and data subject to refutation and confirmation i.e. science.Mark Frank
August 16, 2013
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@ gpuccio Coin-tosses are not relevant. Evolution takes functional proteins and tries minor variations. It does not randonmly assemble sequences from thin air. Also nobody knows how rich in functional proteins the sequence space of all possible proteins is.Alan Fox
August 16, 2013
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Mark: One way of characterising the difference between ID and evolutionary science is that ID is happy to say the designer took care of the poofery end of story while scientists try to find explanations. Well, I would simply say that: a) The emergence of new functional sequences by non design mechanisms against all reasonable odds and against all scientific and empirical credibility is certainly a "poof": functional order coming out without any explanation. The recent debate with some of your side about the belief in "fluke results" here: https://uncommondescent.com/intelligent-design/jerad-and-neil-rickert-double-down/ is a good example. Some "arguments in this thread are another one. The fact remains, believing that function arises without even a trace of explanation about how it arises is believing in a "poof". b) On the other hand, a design explanation is no poof at all. It just means to propose that function arises because a conscious intelligent being inputs purposeful functional order into matter, and that is exactly what we observe in human design. You will certainly object that in the ID scenario we "poof" the conscious intelligent being into existence. We have debated that, and I have tried to show how that "argument" is inevitably dependent on previous ideological commitments about general worldviews. But certainly, if we admit that conscious intelligent beings other than humans, and possibly non physical, may exist, then the ID explanation relies on no "poof" at all. The emergence of functional order from conscious representations is no poof: it is an observed fact.gpuccio
August 16, 2013
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Take a chill pill frank, is this your first time on the internet?
HAH! Again, with your internet dweller memes. It's almost as funny as your nonsense in the above posts. Keep talking AVS, please. Just keep talking.TSErik
August 16, 2013
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One way of characterising the difference between ID and evolutionary science is that ID is happy to say the designer took care of the poofery end of story while scientists try to find explanations.Mark Frank
August 15, 2013
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What about those that deny common descent? As a consequence whole new kinds along with the supporting ecosystems must have poofed into existence!
Great observation! So it makes sense then that all life, if it had been intelligently designed, and specially created -- it stands to reason, by inference, that it happened rather fast, maybe on the order of a few days lest those at the top of the food chain starve, thus the creationists may have a little edge over the front-loaded-evolutionists in the ID community.scordova
August 15, 2013
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You think new genes are poofery. What about those that deny common descent? As a consequence whole new kinds along with the supporting ecosystems must have poofed into existence!Mark Frank
August 15, 2013
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Take a chill pill frank, is this your first time on the internet?AVS
August 15, 2013
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So with every codon, there's less than a 5% chance of it being a stop. Maybe a problem for a 400 amino acid protein, but not for shorter protein sequences.AVS
August 15, 2013
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AVS aka newbie almost a biologist: Eh I took biochem so I have an idea about some of that, but seriously, your point about the small proteins is moot in this conversation. I wanted to create a hypothetical protein chain and I didn’t want it to be short, its that simple. Cool your jets, we get it, youre gonna be counting pills for the rest of your life mr pharm major
You can hamstring your argument in any fashion you like, e.g., as wd400 has pointed out. I think you'll find that there are a lot of folks out there with advanced degrees in Pharmacology and Toxicology that work in a variety of realms outside of the Walmart pharmacy that don't involve counting pills....although there is nothing wrong with that!franklin
August 15, 2013
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Materialists love "poofery." I've been pointing this out for years: https://uncommondescent.com/intelligent-design/materialist-poofery/Barry Arrington
August 15, 2013
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I thought of that, and I dont think its that big of a problem Think harder. If 3/64 triplets encode a stop codon, what do you think the odds of getting a 400 codon long ORF are?wd400
August 15, 2013
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No, that doesnt really help you scor. Especially if when he says "most amino acid sequences arent functional" hes referring to the sequences that are never translated.AVS
August 15, 2013
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AVS, If you took random sequences 1200 nt long you’d almost certainly hit an in-frame stop codon. Even if you didn’t, most amino acid sequences aren’t functional (lots of RNA sequence are though. So it’s unlikely any given random sequences will create a protein. On the other hand, there aren’t all that many ORFans (10-20% is an ascertainment bias since we go out of our way to sequence species from across the tree of life), and many of them likely do have genes as ancestors (which we can’t detect thanks to elevated evolutionary rates) and others can be explained by gene-loss not gene gain. So, we probably don’t need to explain all that many de novo genes origins, but it’s silly to pretend functional sequence would just pop into existence willy nilly.
Thanks.scordova
August 15, 2013
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Eh I took biochem so I have an idea about some of that, but seriously, your point about the small proteins is moot in this conversation. I wanted to create a hypothetical protein chain and I didn't want it to be short, its that simple. Cool your jets, we get it, youre gonna be counting pills for the rest of your life mr pharm major =)AVS
August 15, 2013
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I thought of that, and I dont think its that big of a problem. We need an in-frame stop codon somewhere down the line anyways.AVS
August 15, 2013
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AVS: Shut up frank, youre killing me.
I guess you haven't gotten to the coursework that covers non-bicarbonate buffering capacity (as measured in slykes) or perhaps even allosteric binding and its importance. Maybe a bit of a venture into the realm of pharmacology and its sister science toxicology would expand your horizons!franklin
August 15, 2013
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AVS, If you took random sequences 1200 nt long you'd almost certainly hit an in-frame stop codon. Even if you didn't, most amino acid sequences aren't functional (lots of RNA sequence are though. So it's unlikely any given random sequences will create a protein. On the other hand, there aren't all that many ORFans (10-20% is an ascertainment bias since we go out of our way to sequence species from across the tree of life), and many of them likely do have genes as ancestors (which we can't detect thanks to elevated evolutionary rates) and others can be explained by gene-loss not gene gain. So, we probably don't need to explain all that many de novo genes origins, but it's silly to pretend functional sequence would just pop into existence willy nilly.wd400
August 15, 2013
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Shut up frank, youre killing me.AVS
August 15, 2013
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