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Is the Origin of New Genes “Basically a Solved Problem”?


It is no surprise that proteins—the essential machines of life—are not likely to have evolved. At least, that is, if you believe in science. Even according to evolutionists and the most optimistic assumptions possible, the evolution of proteins is so unlikely it is beyond practical consideration. While this conclusion is intuitive and hardly surprising, there are several reasons for it. One of the reasons is that the scenarios evolutionists typically envision involve the pre existence of proteins. For instance, proteins are needed to create proteins, at least in today’s biological world. Indeed, proteins are also required for life as we know it. So the first proteins would have had to evolved in a very different kind of biological world. Another reason why protein evolution is difficult is that the fitness landscape in protein sequence space is mostly flat and rugged. A few random mutations will quickly degrade protein function and most of the hyper-dimensional sequence space has little or no function and is far from a useful protein. It is extremely difficult for a random sequence to migrate via mutations close enough to a useful protein for natural selection to take over. In fact this challenge makes the protein evolution difficult regardless of whether proteins already exist. But in spite of this problem, evolutionists believe that protein evolution is not a significant problem. Recently an evolutionist commented that it is “basically a solved problem.”  Read more

I just solved the origin of new genes! Is the Origin of New Genes “Basically a Solved Problem”? It is now! Mung
From ‘JUNK’ to Just Unexplored Noncoding Knowledge:...
Interesting acronym: Just Unexplored Noncoding Knowledge (JUNK). Thanks. Dionisio
By the way, the few examples of recent "de novo" gene formation extolled by our darwinist friends seem to emphasize again the fundamental role of transoposons in shaping functional transitions. I am very happy of that because, as many probably know, I have always been a big fan of transposons as engineering tools. Alu repetitive elements are transposable elements which make up about 10% of our genome. They are transcribed, in different modlaities, and constitute about 35% of the transcriptomic pool of repetitive elements. From a darwinist point of view, they could well represent the junkest type of DNA, a proliferation of random transposable elements which started about 80 my ago, before the rodent-primate split. Here is a very interesting paper about Alus and their many possible functions: "From ‘JUNK’ to Just Unexplored Noncoding Knowledge: the case of transcribed Alus" http://bfg.oxfordjournals.org/content/10/5/294.full.pdf+html And here is another interesting paper about Alu positive selection in functional classes of genes: "Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes" http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000610 gpuccio
I must have missed the part where you actually repond to Dr. Hunter’s argument. Is that forthcoming?
Nick Matzke has just admitted that naturalistic evolution has no basis in any known process or science
Why can’t you even get these totally obvious basic points right?
All he has to offer are ad hominems and irrelevancies. By pointing to the obvious and trivial and implying we are ignorant, he is saying that he has nothing. Nick, why not be gracious and admit this? jerry
As Dr. Hunter alluded to, the 'gene' is certainly far more complex that is was originally envisioned to be by Darwinists, (or by anyone else for that matter). In fact, in terms of complexity, it is far, far, beyond any Computer program or Computer-Aided Manufacturing (CAM) built by man. Moreover, the very definition of the gene, due to the overlapping intergrated complexity been dealt with, is being hotly debated,,
The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin https://vimeo.com/106012299 "Sixty years on, the very definition of 'gene' is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level." (DNA at 60: Still Much to Learn April 28, 2013) http://www.scientificamerican.com/article.cfm?id=dna-at-60-still-much-to-learn Further Thoughts on the ENCODE/Junk DNA Debates - James Shapiro - Sept. 18, 2012 Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of "DNA Elements" rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries. http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.,,, Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously, with a plateau at about 10–12 expressed isoforms per gene per cell line. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html Alternative Splicing: The Film Editor of the Genome - September 9, 2014 Excerpt: The story compares alternative splicing (performed by a sophisticated molecular machine, the spliceosome) to what a movie editor does: "Film editors play a critical role by helping shape raw footage into a narrative. Part of the challenge is that their work can have a profound impact on the finished product -- with just a few cuts in the wrong places, comedy can become tragedy, or vice versa. A similar process, "alternative splicing," is at work inside the bodies of billions of creatures -- including humans. Just as a film editor can change the story with a few cuts, alternative splicing allows cells to stitch genetic information into different formations, enabling a single gene to produce up to thousands of different proteins." http://www.evolutionnews.org/2014/09/alternative_spl089421.html Design In DNA – Alternative Splicing, Duons, and Dual coding genes – video (5:05 minute mark) http://www.youtube.com/watch?v=Bm67oXKtH3s#t=305
also see James Shapiro,, bornagain77
gpuccio, Those proteins are far to old. We need something newer. Can't you find any proteins that recently evolved, say maybe last thursday or thereabouts? Mung
Even Michael Behe and David Berlinski agree that natural evolutionary processes can create new genes. Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003. Why can’t you even get these totally obvious basic points right?
I must have missed the part where you actually repond to Dr. Hunter's argument. Is that forthcoming? Mung
When will Nick please publish his book on macro evolution? Andre
And in all that stuff it collected that doesn’t kill it, there will be stuff that just goes together and starts functioning. There’s bound to be an ATP synthase in there somewhere.
LOL. Like a pile of rocks. There's always something really good in there. We usually find something just like an ATP synthase, but a little simpler - you know, like big rocks and small rocks. And genetic stuff is even better than that because when it piles up, it just starts functioning all of a sudden. To Dr. Matzke's credit, I'm just glad we can still find someone who's got the courage to publicly defend Darwinian theory. Or maybe it's all just a satire? He really works for the DI and he's paid to entertain us? Silver Asiatic
Joe: You are very convincing, maybe you should switch to the other field (but try to be payed well for that!) :) gpuccio
Dear gpuccio- (sarcasm warning) ATP synthase is too specific. Evolution doesn't work like that- there isn't any search for any specific target. The process just runs and if it happens to collect stuff that works, great. If it collects stuff that kills it, well, that's bad, OK. But the main part is the stuff that works or at least isn't fatal. That can just grow like Nick's rock pile or a stalagmite. Rock piles can spread out and function as a dam, as long as there is something to dam. So it is with life. It just chugs along collecting stuff until it can't. And in all that stuff it collected that doesn't kill it, there will be stuff that just goes together and starts functioning. There's bound to be an ATP synthase in there somewhere. That is the stuff of life under evolutionism. Joe
Dear bornagain77- Please stop slapping the guests around with the facts. Have you no decency, sir? :cool: Joe
Luskin’s main complaint about the Cheng, et al. paper is that it invokes various processes (known to occur in nature) to account for the end product:
Computers run by various processes known to occur in nature. Cars do too. The question is are those various processes known to occur in nature also produced by nature, operating freely? Artifacts are known to occur in nature but they are never produced by nature. Joe
Long et al. claim that jingwei is only 2.5 million years old, but the original study compared the Adh-like exon in jingwei with the allegedly ancestral exon from Adh and found that they were so different that they must have diverged at least 30 million years ago.
Thats how they figured out selection was at work. Derp. Starbuck
Luskin’s critique is ridiculous from top to bottom: http://www.pandasthumb.org/arc.....-th-2.html
Wow - that was a response to Luskins critique? Hilarious. It says nothing.
...Casey Luskin, attack gerbil of the Disco ‘Tute, invokes Stephen Jay Gould’s infamous “just so” phrase.
When you don't have a response, maybe ridicule will work.
The parallel case is accounting for how a particular boulder, indicated below by the red arrow, got to where it was in a landslide (image used by permission of Air-and-Space Museum).
LOL -- compare homology within a complex biological system to the position of boulder and a nearby ledge. That's how incredibly stupid the Darwinian ideologues actually are. Amazing. As if the construct of a genetic code is as obvious as a boulder rolling off a cliff. Good example! A pile of rocks after an avalanche. Sure! It's just about the simple as a celluar function and just as easy to explain! Hahahahahaha.
Luskin’s main complaint about the Cheng, et al. paper is that it invokes various processes (known to occur in nature) to account for the end product:
"Known to occur" -- um yes, but "not known to produce new genes". :-)
Whenever you find shape and mineral composition homology between a rock at the bottom of a slope and a ledge up the slope, just invoke a hypothetical breakage event
Ok, I'm supposed to take this seriously. Of course, since it came from Panda's Thumb it must be "real science".
...we just invoke hypothetical breakage and landslide events to account for the boulder’s existence and position, using the magic wand of gravity as a natural law in our explanation.
I love it. Natural selection is more certain than gravity. In the same way that rocks roll off of ledges, mutations create new genes. It's obvious! :-)
To account for the driving force that got it to its position at the bottom of the slope just invoke the magic wand of gravity.
To account for the origin of a gene, find one that looks like it and then say it evolved from that one. No need for the magic wand of Darwinian selection at all. If a scientist makes the claim, then it must have happened that way, right?
And, why should I take any of your skepticism seriously, when Behe himself, your guys’ highest authority, agrees that natural processes can produce new genes, even new gene essential to the organism?
Personally, just because Michael Behe said it, doesn't mean I need to agree. For me it's not an argument from authority, but anyway, I'd expect you to come up with something a lot more convincing than what you posted. If that's your best evidence, I'd say you're light-years away from meeting the challenge of explaining any kind of evolutionary origin for proteins. It's a massively difficult task. I think you'd need to take that seriously because right now, you' have very little from the Darwinian perspective to work with. Silver Asiatic
Dr. Matzke claims,,,
Even Michael Behe and David Berlinski agree that natural evolutionary processes can create new genes. Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003.
Yet Berlinski is hardly in agreement with Matzke and, in fact, Berlinski thinks Mazke 'hopeless' for citing Long's paper as evidence for neo-Darwinian evolution,,
Hopeless Matzke - David Berlinski & Tyler Hampton August 18, 2013 Excerpt: In 2003, Long et al. published an interesting paper entitled "The origin of new genes."1 It is this paper to which Matzke appeals, often with satisfaction, always with assurance. Long et al. argued that the genes Sdic, Sphinx, Jingwei, RNASE1, and AFGP, among others, have originated, or evolved, within the last few million years, and this by what is essentially the old fond familiar process of typographic variation within the genome: Cut, Snip, Fiddle, Transpose, Shuffle, Replace. It is easy to see why Old Believers should find this paper rewarding. It looks so simple. Those unforthcoming facts: In every example cited by Long et al., nothing like a new protein structure is in evidence; Long et al. remain throughout within the ambit of Small Time innovations, and from this ambit, they never depart: 1) Sdic A recently evolved chimeric gene encoding a protein in the species Drosophila melanogaster. Considering the order and sequence similarity of the surrounding genes, AnnX and Cdic, it is both easy and invigorating to imagine a process of duplication, deletion, fusion, and sequence rearrangements transforming AnnX and Cdic into Sdic.12 Matzke says as much: He has lovely colored pictures to pass around. His analysis has been corrupted throughout by a systematic equivocation between genetic novelties and novelties in protein chemistry. The first is no good guide to the second. Cdic is a gene encoding a dynein intermediate polypeptide chain, one expressed in the cytoplasm. But Sdic also encodes a dynein-specific intermediate folding chain, one expressed in the testis. Save for the fact that it is truncated at the N-terminal, Sdic has the same structure as Cdic. It is expressed in sperm because the gene has acquired a new promoter from its fusion with AnnX. The argument at issue concerns enzyme specificity and novel protein folds, not promoters and expression patterns. In a stimulating paper entitled "Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition," Shu-Dan Yeh et al. reported on work in which they deleted the region of the chromosome containing Sdic copies in order to test the effect of Sdic on fitness.13 They subjected male flies with and without Sdic to mating rounds with females. The results were anything but provocative, least of all to the flies, and not at all to Shu-Dan Yeh et al. There was no discernable effect on the fly phenotype. Under benign conditions, those individuals without Sdic left as many progeny as those with Sdic. In multiple rounds of mating, when a female was first subjected to a mutant male without Sdic, and then one with, the presence of the gene gave no statistically significant advantage in sperm displacement. Repeating the experiment in reverse did lead to an advantage, but the relevance of this result to any larger issue of principle remained obscure. This is where it remains today. The emergence of Sdic thus suggests a weak form of microevolution, so weak as to be embraced with equanimity by those proposing to champion, and those prepared to deny, the power of Darwinian theory. A protein dispensable to function, uninteresting in its chemistry, and with no control over morphology, has evolved by stochastic means. Whoever thought to deny it? The lysyloxidase family is otherwise. Big difference.,,,, 3) Jingwei Well known for being well known, Jingwei is a chimeric gene made from the Alcohol Dehydrogenase (Adh) gene and another called yande. The protein expressed by Jingwei is a member of the broad and noble class of enzymes that degrade alcohol (friends to humanity, if nothing else). Its parent gene, Adh, serves the same function. In a paper to which Long is a contributor, Jiaming Zhang et al. remark that Drosophila ADH belongs to the short-chain dehydrogenase/reductase (SDR) family ... SDRs share a common protein fold, consisting of a central ?-sheet surrounded by ?-helices and a typical nicotinamide coenzyme binding ????? subdomain, with a characteristic Gly-Xaa-Gly-Xaa-Xaa-Gly motif ... Asp-37 confers specificity toward NAD binding, whereas the active site is characterized by a Ser-Tyr-Lys catalytic triad .... These and other conserved SDR features are preserved in JGW ..." The familiar deflationary wheeze now follows: "We predict that JGW will retain NAD-specific dehydrogenase activity" (emphasis added).16 No new folds. No new structures. No new nothing. But, of course, something slightly different. When compared to AdH, it is plain enough that Jingwei is both more effective and more specific in degrading long-chain alcohols. These modest improvements in specificity did not simply emerge all at once, like Venus emerging from a clamshell in Botticelli's famous painting: Adh encodes a polypeptide that can metabolize a diverse range of alcohols as well. Jingwei thus augments the functions of an ancestral AdH enzyme. "Substrate specificity of JGW," Jiaming Zhang et al. write, "was further characterized in a survey of 34 alcohols that included representatives from all major classes found in nature ... Like ADH, JGW shows activities toward a broad range of alcohols. However, compared with ADH, JGW also shows a systematic preference for long-chain primary alcohols and increased specificity... including farnesol and geraniol ... These results confirm that JGW has evolved altered specificity after diverging from its parental genes, Adh and ynd."17 Improvements? Yes. Structural innovations? No. Relevance? None.,,, http://www.evolutionnews.org/2013/08/hopeless_matzke075631.html
Thus Matzke, besides his long history of literature bluffing, which he is notorious for, has now apparently taken it upon himself to dishonestly claim that ID proponents hold positions that they do not hold.,,, bornagain77
Joe: You are absolutely right. Nick Matzke obviously does not understand the problem. It is perfectly clear that new genes evolve. Form where does he think that we believe all the existing genes came? But that "natural evolutionary processes" can create them, that is all another matter. Moreover, it is perfectly obvious, as Behe says, that "natural processes can produce new genes, even new genes essential to the organism", provided that those genes arise through a simple transition. The problem of exon sfhuffling and of remixing of existing information is complex, and I think we don't know enough at present to understand if some simple cases could be explained as random events, while others (most certainly) cannot. I don't remember, however, Nick Matzke (or anyone else, for that) proposing such a theory for the origin of ATP synthase. Am I repeating myself? Yes, I am. :) gpuccio
Look we've got one of the dirt worshipping disciples commenting here himself. Obviously Cornelius said something about his religion that has left him frothing at the mouth. That means whatever was said must be true. Nick, the law will only protect your religion for a little while more and then it will be tickets for god Darwin and his blind cult followers. Enjoy it while it lasts.... Andre
What Behe says is that genes can evolve if there is probabilistic pathway, however, in reality such pathways are extremely limited as is reflected by the evidence. What you claim is that everything evolved, and who cares how ridiculous the pathway is or how many improbable neutral or deleterious steps it takes to get there, and never mind the mathematical impossibilities, just say it evolved and force the schools to teach that to the children without question. As Cornelius points out, the probability of a novel gene evolving is so remote as to be impossible, especially when one regards abiogenesis scenarios. The fact that you can tell a crazy story about jingwei proves nothing. There is difference between science and making stuff up. Jehu
NickMatzke- Please tell us how it was determined that gene duplication followed by function altering changes is a blind watchmaker process. ID is not anti-evolution, NickMatzke. ID says that organisms were designed to evolve and evolved by design. Let's see how the next court case deals with that fact. Joe
Luskin's critique is ridiculous from top to bottom: http://www.pandasthumb.org/archives/2011/01/casey-luskin-th-2.html And, why should I take any of your skepticism seriously, when Behe himself, your guys' highest authority, agrees that natural processes can produce new genes, even new gene essential to the organism? NickMatzke_UD
jingwei http://www.nature.com/nrg/journal/v4/n11/box/nrg1204_BX1.html "A portion of jingwei was found to be a homologue of the Adh gene ..." Homologue. How much more evidence do you want? It looked very similar and therefore it evolved by natural selection. Totally obvious. I liked the commentary on Biologos that showed concern about the scientific community's efforts to offer believable explanations of evolution theory to the general public. Perhaps scientists could do a better job in ridiculing and insulting people who find their speculations unconvincing. Mandatory evolution-education in schools has rendered us ignorant about evolution, apparently. Or better yet, we're "fundamentalists" so what can you really expect? I guess there's nothing much to wonder about here -- it's all a solved problem at this point. a. Jingwei The first entry in the table comes from a study that Long co-authored with Charles Langley in Science. The study asserts that a fruit fly gene, jingwei, arose when part of another gene, Adh, was retrotransposed into a new location on a fruit fly chromosome near a duplicate of the gene yellow-emperor.45 Their evidence for this rearrangement is sequence similarity between part of jingwei and Adh, and part of jingwei and yellow-emperor. Thus, invoking Gene Evolution Game Rules 1 and 3, the authors tell a story that presumes that hypothetical duplicates of yellow-emperor and Adh were fortuitously spliced together to create a new functional gene—jingwei. The exact word used is that exons were “recruited” from elsewhere into the genome “by capturing several upstream exons and introns of an unrelated gene” to produce “a new functional gene.” They author make no attempt to address the more important questions, such as whether a step-wise path to such a genomic rearrangement could have happened by unguided chance to fortuitously produce this gene. Merely finding sequence similarity between exons and other genes (or pseudogenes) does not thereby demonstrate neo-Darwinian evolution. Long et al. claim that jingwei is only 2.5 million years old, but the original study compared the Adh-like exon in jingwei with the allegedly ancestral exon from Adh and found that they were so different that they must have diverged at least 30 million years ago. This poses a problem, because this fruit fly clade is not thought to be nearly that old; as Long and Langley write, “This conflicts with the age of the melanogaster subgroup, which is estimated to be 17 to 20 million years.” More important, the unexpectedly high degree of differences between the exons is taken, under neo-Darwinian assumptions, as evidence that jingwei “responded to positive natural selection and evolved a new function.” Yet according to one commentator, despite the fact that they are sure natural selection drove this gene to acquire its new function, “its actual function is obscure.”46 So they claim that natural selection was the driving mechanism, but they do not even know for sure in this paper that the gene has a function. They have not addressed any of the deeper questions of gene evolution, instead offering an incomplete and assumption-based story that ignores warnings from Austin Hughes against invoking “positive selection divorced from any biological mechanism.”47 http://www.ideacenter.org/contentmgr/showdetails.php/id/1501 Silver Asiatic
Cornelius Hunter is responding to me. My reply: Even Michael Behe and David Berlinski agree that natural evolutionary processes can create new genes. Look up jingwei and sdic and the literature on their origin. Look up Long et al. 2003. Why can't you even get these totally obvious basic points right? NickMatzke_UD
As with any number of other things, if Evolution were a valid theory, we should see new proteins appearing in the absence of cellular life. And I haven't heard of anyone stumbling on such things. Of course one can assert that the Early Earth was a different place, where magic still worked and unicorns and Leprechauns frolicked on the barren rocks... But at some point you have to admit that assigning an event to "magic" is not any solid logically than admitting that the SIMPLE solution requires a Designer. mahuna
OK, maybe our darwinist friends are tired of hearing me about ATP synthase. I can understand that. So, shall we try something else? Let’s say the conserved proteins in Photosystem II, between cyanobacteria and flowering plants?
:) Dionisio
mk: Well said. I stick to my classical example: the alpha and beta sububnits of ATP synthase. Old protein, has been there practically from the beginning. About 370 identities between bacterial, archeal and human form of the protein. That means about 1600 bits of minimal functional information (about 1:10^480 probability of the functional form). OK, maybe our darwinist friends are tired of hearing me about ATP synthase. I can understand that. So, shall we try something else? Let's say the conserved proteins in Photosystem II, between cyanobacteria and flowering plants? I am ready, if they are interested. gpuccio
a tipical protein is about 300 aa with 20^300 possiblle sequences. lets say that only 1\3 of the protein is need for is minimal function. this give us a 100 aa for minimal function or 20^100. lets say that the number of functional protein is more than 10^10 of functional sysyems that intellegent desing can made(human). that give us more then the number of atoms in the universe(mutations) for functional protein. even if we consider the synonyms of the dna. i challenge any evolutionst. isoryy for my english. mk

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