Forget the selfish gene; no, no, it’s the ribosome that’s selfish, say researchers

So Dawkins books can be moved to the fantasy section finally where they have always belonged. Keep a space open for origin of the species... Can't be long now. humbled

Nucleotide composition of cellular internal ribosome entry sites defines dependence on NF45 and predicts a posttranscriptional mitotic regulon. doi: 10.1128/MCB.00546-12 The vast majority of cellular mRNAs initiate their translations through a well-defined mechanism of ribosome recruitment that occurs at the 5'-terminal 7-methylguanosine cap with the help of several canonical protein factors. A subset of cellular and viral mRNAs contain regulatory motifs in their 5' untranslated regions (UTRs), termed internal ribosome entry sites (IRES), that sidestep this canonical mode of initiation. On cellular mRNAs, this mechanism requires IRES trans-acting protein factors (ITAFs) that facilitate ribosome recruitment downstream of the cap. While several ITAFs and their target mRNAs have been empirically identified, the in silico prediction of targets has proved difficult. Here, we report that a high AU content (>60%) of the IRES-containing 5' UTRs serves as an excellent predictor of dependence on NF45, a recently identified ITAF. Moreover, we provide evidence that cells deficient in NF45 ITAF activity exhibit reduced IRES-mediated translation of X-linked inhibitor of apoptosis protein (XIAP) and cellular inhibitor of apoptosis protein 1 (cIAP1) mRNAs that, in turn, leads to dysregulated expression of their respective targets, survivin and cyclin E. This specific defect in IRES translation explains in part the cytokinesis impairment and senescence-like phenotype observed in HeLa cells expressing NF45 RNA interference (RNAi). This study uncovers a novel role for NF45 in regulating ploidy and highlights the importance of IRES-mediated translation in cellular homeostasis. http://www.ncbi.nlm.nih.gov/pubmed/

Dionisio

Tempo and mode of gene duplication in mammalian ribosomal protein evolution [?] doi: 10.1371/journal.pone.0111721 Gene duplication has been widely recognized as a major driver of evolutionary [?] change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution [?] of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution[?]. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising* due to the fact that ribosomal protein genes evolve [?] slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution [?]. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected* retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism. http://www.ncbi.nlm.nih.gov/pubmed/25369106

Was this the best 'persuading'/'convincing' argument they could produce less than 3 months ago? :) PS. (*) surprising, unexpected? why? what did they expect instead? Dionisio

Specialized ribosomes: a new frontier in gene regulation and organismal biology doi: 10.1038/nrm3359. Historically, the ribosome has been viewed as a complex ribozyme with constitutive rather than intrinsic regulatory capacity in mRNA translation. However, emerging studies reveal that ribosome activity may be highly regulated. Heterogeneity in ribosome composition resulting from differential expression and post-translational modifications of ribosomal proteins, ribosomal RNA (rRNA) diversity and the activity of ribosome-associated factors may generate 'specialized ribosomes' that have a substantial impact on how the genomic template is translated into functional proteins. Moreover, constitutive components of the ribosome may also exert more specialized activities by virtue of their interactions with specific mRNA regulatory elements such as internal ribosome entry sites (IRESs) or upstream open reading frames (uORFs). Here we discuss the hypothesis that intrinsic regulation by the ribosome acts to selectively translate subsets of mRNAs harbouring unique cis-regulatory elements, thereby introducing an additional level of regulation in gene expression and the life of an organism. http://www.ncbi.nlm.nih.gov/pubmed/22617470

Dionisio

RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation doi: 10.1038/nature14010. Emerging evidence suggests that the ribosome has a regulatory function in directing how the genome is translated in time and space. However, how this regulation is encoded in the messenger RNA sequence remains largely unknown. Here we uncover unique RNA regulons embedded in homeobox (Hox) 5' untranslated regions (UTRs) that confer ribosome-mediated control of gene expression. These structured RNA elements, resembling viral internal ribosome entry sites (IRESs), are found in subsets of Hox mRNAs. They facilitate ribosome recruitment and require the ribosomal protein RPL38 for their activity. Despite numerous layers of Hox gene regulation, these IRES elements are essential for converting Hox transcripts into proteins to pattern the mammalian body plan. This specialized mode of IRES-dependent translation is enabled by an additional regulatory element that we term the translation inhibitory element (TIE), which blocks cap-dependent translation of transcripts. Together, these data uncover a new paradigm for ribosome-mediated control of gene expression and organismal development. http://www.ncbi.nlm.nih.gov/pubmed/25409156

Dionisio

OK, so now the latest and greatest idea is the selfish ribosome. How long will this one last? Any guesses? Anyone want to explain where that came from? Probably more magical hand waving and all of a sudden a ribosome emerges. Real scientific answer! tjguy

jstanley01 # 7

“Scientifically” think, as opposed to “erroneously” think? “Presumptuously” think? “Pedantically” think? “Anthropomorphically” think? “Unjustifiably” think? “Laughably” think? “Disingenuously” think? “Propagandistically” think? Any creative writer who appreciates the contribution that free association exercises make to his or her routine pursuits of communicating just the right nuances in what he or she writes, soon develops a heartfelt love for adjectives’ ability to put various (not to mention sundry) spins on simple nouns like “think.”

please forgive my silliness, but i was following the lead af goodusername's use of his own chosen adverb to the verb think when he wrote: "it can be useful to metaphorically think of genes as selfishly wanting nothing more than to replicate themselves and spread throughout a population" btw, i'm pretty sure we're actually using adverbs to spin the verb think, and not adjectives on a noun, as you wrote. awstar

Well, the selfish gene IS Neo-Darwinism. So, are we finally allowed to stop pretending Neo-Darwinism has any life left in it? Or are the thought police going to tell us we have to keep in line and stop appealing to evil things like thinking for oneself, evidence, analysis and rationale? "Can things without minds want things, and if not, why is it helpful to speak of them as if they do?" Selfish ribosome is still Gestalt Magic not science. First, Logic: 1.) The cosmos contain humans. 2.) Humans have mind, intelligence, foresight, agency, freewill, desire, passion, etc. 3.) The cosmos contain mind, intelligence, foresight, agency, freewill, desire, passion, etc. No matter how you slice it, rephrase it, or dodge it, the cosmos have been imbued with mind, intelligence, foresight, agency, freewill, desire, passion, etc. at the very least in part. That being said, unless we find a good explanation for subatomic particles carrying these characteristics, then we MUST give up the charade that Reductionism will yield any tenable result in the understanding of the human condition (this includes biology). Thus far methodological naturalism is tying itself in knots because we know as incontestable truth that elements necessarily radioactively decay. The jump to biological creatures insisting against thermodynamic laws that they must perpetuate themselves by clamoring to keep more or less the same elemental makeup is Gestalt Magic. Gestalt Magic is a better explanation for life than Intelligence? Sad. Also, all last year I insisted that any Nick Matzke-like individual who understands macroevolution should be able to predict for us the next season's flu strains. No one took up the challenge, because, after all, we understand so little about even this microevolutionary process on such a small timescale that we can't predict jack: http://www.naturalnews.com/047890_flu_vaccines_CDC_apology_medical_fraud.html. But, of course, we all must keep faith in macroevolution despite the science; and now when going down to the abject failure of OOL research we just gotta keep the faith that a selfish ribosome or selfish something else will bridge the empirical gap which cannot ever be filled. Just keep the faith! Go Darwin! Let's keep grinding scientific discovery to a painful halt with adherence to an obscure discredited ancient belief system popularized by a 19th century depressed, anxious, agoraphobic, neurotic, racist invalid who sought the counsel of clairvoyants and mesmerists (http://en.m.wikipedia.org/wiki/Charles_Darwin%27s_health). Yay! *palm to forehead* jw777

The selfish gene is certainly the natural extension of the theory of natural selection. However, the evidence coming in of the complex relationships between genetic and epigenetic data -- factored in with environmental conditions leaves very little room for natural selection to select for a beneficial genetic mutation, doesn't it. Unfortunately, what we learn from neutral theory is that even mildly deleterious mutations can become fixed. This picture is really really bad for the synthesis. Moose Dr

goodusername: Again, it can be useful when explaining what to expect of certain things in nature.

Our concern is raised when it is used by materialists to "explain" what materialism cannot explain. Used to "explain" things that cannot be expected from atoms and molecules; like purpose, decisions, self-organization and ‘selfishness’. Box

News,

goodusername at 2: Can things without minds want things, and if not, why is it helpful to speak of them as if they do?

Again, it can be useful when explaining what to expect of certain things in nature. And so one routinely hears in chemistry and physics courses about happy hydrogen atoms and carbon atoms ”trying” to combine with other atoms, and “nature abhorring a vacuum.” Although there may be drawbacks. to such language. goodusername

awstar @ 3 wrote:

it can be useful to scientifically think of genes as selfishly wanting nothing more than to than what they have been designed to do, including dying it the appropriate time.

"Scientifically" think, as opposed to "erroneously" think? "Presumptuously" think? "Pedantically" think? "Anthropomorphically" think? "Unjustifiably" think? "Laughably" think? "Disingenuously" think? "Propagandistically" think? Any creative writer who appreciates the contribution that free association exercises make to his or her routine pursuits of communicating just the right nuances in what he or she writes, soon develops a heartfelt love for adjectives' ability to put various (not to mention sundry) spins on simple nouns like "think." jstanley01

Their animist belief is not something they are proud of, nor the fact that they have been 'forced into it' in desperation, so it is not entirely true that they are without shame. Axel

Even in an unicellular organism we witness purpose, self-organization and indeed 'selfishness'. It is exactly this 'self' - something with decision power - that cannot be explained under materialism. So what to do? Point to some part of the cell and hypothesize that it contains (or is equal with) a self. Epigenetics invalidated the 'selfish gene' (aka the central dogma, DNA -> RNA -> Protein), because it showed that DNA is not a self-regulator, but instead is regulated by many other factors. I predict that this will prove to be true for the ribosome as well. IOW there is no material self-regulator (no unmoved-mover, no self, no person) to be found in the cell. S.L.Talbott put it like this:

When regulators are in turn regulated, what do we mean by “regulate” — and where within the web of regulation can we single out a master controller capable of dictating cellular fates? And if we can’t, what are reputable scientists doing when they claim to have identified such a controller, or, rather, various such controllers? If they really mean something like “influencers,” then that’s fine. But influence is not about mechanism and control; the things at issue just don’t have controlling powers. What we see, rather, is a continual mutual adaptation, interaction, and coordination that occurs from above. That is, we see not some mechanism dictating the fate or controlling an activity of the organism, but simply an organism-wide coherence — a living, metamorphosing form of activity — within which the more or less distinct partial activities find their proper place. The misrepresentation of this organic coherence in favor of supposed controlling mechanisms is not an innocent inattention to language; it is a fundamental misrepresentation of reality at the central point where we are challenged to understand the character of living things.

Box

goodusername at 2: Can things without minds want things, and if not, why is it helpful to speak of them as if they do? Metaphors can mislead, and anthropomorphic metaphors are especially liable to that problem. Most of the nonsense around evolutionary psychology derived explicitly from attempting to treat genes instead of minds as strategists and decision-makers. By the time evo psych was right up there with Freud, it was on the way out, by the same door. News

goodusername #2

it can be useful to metaphorically think of genes as selfishly wanting nothing more than to replicate themselves and spread throughout a population

it can be useful to scientifically think of genes as selfishly wanting nothing more than to than what they have been designed to do, including dying it the appropriate time.

We, alone on earth, can rebel against the tyranny of the selfish replicators.

Sounds like this evidence better supports the belief that the human mind may be in the brain, but it wasn't created by the brain. Just as real science shows that information may be held in molecules, but information is not created by molecules, only by intelligent agents. A ribosome may indeed be an intelligent agent, but who gave it it's intelligence? awstar

News:

Can things without minds want things, and if not, why is it helpful to speak of them as if they do?

Because in thinking about what sort of mutations are likely to be successful and which aren't, it can be useful to metaphorically think of genes as selfishly wanting nothing more than to replicate themselves and spread throughout a population.

...researchers and journalists who scoff at the idea that humans are motivated by their genes and not by their own free will.

To be "motivated by their own free will" doesn't make any sense to me. What sort of motivations come from free will? Motivations come from desires, which certainly have a genetic component. Free will is the ability to choose how to act on those desires.

Maybe the actual aim of the selfish gene idea wasn’t so much to elevate the gene as to denigrate the mind, as an actor in human affairs?

I'm not sure how the idea of the selfish gene does anything to denigrate the mind. It's simply part of the debate as to what is the most important unit of selection (the gene versus the organism versus the group, etc). Besides, does this look like someone denigrating the mind: “We, alone on earth, can rebel against the tyranny of the selfish replicators.” goodusername

Next up, The Selfish Membrane. Still a mystery for those who embrace science and reject "it just happened. that's all" metaphysics. Mung