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Uncloaking The Factless Guesswork Of Evolution’s Intron-Splicing Magic

Shattered assumptions, broken rules and overturned beliefs.  The science media seems eager these days to emphasize science’s capacity to shift paradigms.  And it was such a handful of descriptives that was used to convey the implications of a new study that redefines our view of genome architecture (1).  At the heart of such excitement lay a tunicate organism called Oikopleura dioica that carries in its genetic armory “several peculiarities” (1).  Weighing in with its 70 million base pairs of DNA Oikopleura is today venerated as the animal with the smallest known genome (1).  But what stands out for biologists who have dedicated years to unpacking Oikopleura’s treasure box genome is the ‘odd ball’ physical location of many of its genes (1).  The Scientist’s Megan Scudellari remarked that “Oikopleura’s genes appear to have been shuffled like a deck of cards” (1).

At the apex of this presumed shuffling is that all-elusive but much loved patch-all process called evolution.  “UV rays and other mutagens” that bombard Oikopleura as it ekes out its existence just below the ocean surface are the suggested deck dealers of this particular shuffle (1).  But apart from this rather misty association between cause and effect, there is precious little in the evolutionary inferences of this study to satisfy an appetite for robust scientific argumentation.  To be fair, there are observable facts that we can latch onto and embrace as the products of rigorous science:

(i)            Oikopleura’s genome is extremely small containing the same number of genes found in humans (18,000) but compacted into a genome that is 1/40th of the size (1).  Genome compactness is reflected in small intergenic distances (53% are less than 1Kb)(2).

(ii)           While the Oikopleura external phenotype is clearly in line with that observed in other tunicates, the intronic organization of its genome is vastly different (introns are very small peaking at 47 base pairs in length)(2).

(iii)          Oikopleura is unique amongst the tunicates in having both male and female individuals (2).

(iv)         Oikopleura exhibits high mutation rates and low dN/dS ratios per each 4-day long generation (dN and dS being the rate of substitutions in non-silent and silent sites respectively)(2).

But there is also fact-less guesswork.  For example, since this new study found that many of Oikopleura’s introns display high sequence homology, the follow-on assertion put forth by the authors is that introns multiplied in the genome in a hap stance, “by chance” fashion and that genome architecture across the animal kingdom is therefore inherently plastic and unconnected to morphological/developmental complexity (1,2).  Such a grossly overstated endpoint does not appear to be supported by anything close to a thorough examination of intron location and animal morphological variability. 

Twenty years ago scientists began to understand the intimate role that introns play in gene regulation in higher order animals (3).  We now know that intron splicing involves “the precise deletion of an intron from the primary transcript” so that exons on either end can be joined in readiness for protein translation (4).  The choice of specific splice sites depends on the surrounding sequence and structure of the RNA (5).  Three types of sequence- the 5’ splice site, the 3’ splice site and a branchpoint sequence- are almost invariably found in pre-mRNA introns of higher eukaryotes although these elements alone are insufficient to account for the specificity of the splicing reaction (5).  Additional signals in abutting exons not only ensure that accurate splicing is maintained but also prevent exon ‘skipping’, which would of course adversely impact the functionality of the translated product (6). 

In some cases more than one mRNA can be coded for by a “single stretch of DNA” as a result of different splicing pathways, different intron cleavage sites and selectively active promoters (3).  The mouse salivary amylase gene is perhaps the archetypal example of the multi-variant role that introns play in gene regulation.  In this instance alternative but nevertheless nucleotide-specific splice sites are used depending upon whether expression is required in salivary glands or the liver (3).  Stephen Meyer writes: “like Russian dolls stored within Russian dolls, exons and introns encode multiple genetic messages within themselves and are themselves part of a larger genetic message” (7).

Genomic mapping has shown that “of 5589 introns mapped by interspecies protein alignments, 76% had positions unique to Oikopleura” (2).  It is therefore assumed evolutionarily speaking that Oikopleura’s single major spliceosome made up of U1 snRNP and U2AF proteins, is capable of recognizing donor and acceptor sites in the genome and shuffling introns around accordingly (2).  Such a proposed transposition and propagation seems to fly in the face of what we know about the contextual requirements of intron splicing as outlined above.  For instance, if differing intron splicing pathways are active in distinct parts of an organism then we would expect their transposition to novel genome sites to be extremely disruptive to gene function within their new context. 

Evolutionists’ intron-splicing magic is rife with factless guesswork.  Even the briefest of considerations as is offered here makes that plain.

 .Further Reading

  1. Megan Sculellari (2010) Who Needs Structure Anyway? The Scientist, 18th November, 2010, See http://www.the-scientist.com/news/display/57814/
  2. France Denoeud et al (2010) Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate, Science, Vol 330, pp.1381-1385
  3. Benjamin Lewin (1990), Genes IV, Oxford Cell Press, pp.484-486
  4. Christopher Wills (1991) Exons, Introns & Talking Genes: The Science Behind The Human Genome Project, Oxford University Press, Oxford UK, p.112
  5. Adrian Kramer & Tom Maniatis (1990) RNA Splicing, in Transcription And Splicing, Eds B.D. Hames & D.M. Glover, IRL Press, Washington DC, pp.141-145
  6. Ibid. p.159
  7. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.463
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16 Responses to Uncloaking The Factless Guesswork Of Evolution’s Intron-Splicing Magic

  1. I’ve often thought that looking at a genome and nucleotide/amino-acid sequences might be somewhat analogous to looking at the compiled and linked binary code of a computer program. Very different programs would have much in common.

    All of the bytes, words, and long words associated with the CPU instruction set would be identical. Calls to the operating system for many processes (e.g., memory access and disk I/O) would result in similar or identical binary code. At a higher level, many algorithmic processes (e.g., sorting routines like QuickSort) would be shared by programs as disparate as spreadsheets, word-processors, AI chess engines, and video editors.

    Many more examples could be given.

    If one were to look only at the compiled binary code (the genome) he might easily come to the conclusion that the code had been “shuffled like a deck of cards.” However, if one had access to the commented source code, it would quickly become apparent that the entire thing was designed from the top down, and was not the result of an accident from bottom-up random tinkering.

    The mixing, matching, and clever rearrangement and integration of much extant code, plus the introduction of some novel code, would be seen to explain what is going on. And what is going on would clearly require design.

  2. Genetic Discoveries Uproot Darwin’s Tree Of Life – Video
    http://www.metacafe.com/watch/5710852/

  3. Editing and splicing require knowledge- knowledge of what is to edited/ spliced, knowledge of how to edit/ splice, knowledge of when to edit/ splice, etc.

    To think that blind, undirected (chemical) processes can pull off such a feat is nothing but a belief in magic.

    And that is why we have “Poof, the Magic Mutant”…

  4. To think that blind, undirected (chemical) processes can pull off such a feat is nothing but a belief in magic.

    For me, something like the opposite is the case. If chemical processes are able to pull off such feats, maybe they aren’t so blind or undirected after all, eh?

  5. nullasalus:

    If chemical processes are able to pull off such feats, maybe they aren’t so blind or undirected after all, eh?

    Badda-bingo!

    That is the point- Intelligent Design is already in biology textbooks- meaning we don’t need to teach ID in biology classrooms, we just need to stop with the nonsense of telling kids that a) all mutations and genetic changes are accidents/mistakes/ errors and b) teleology is not required.

    If that happened the kids would clearly see we live in an engineered world. :cool:

    But I am sure the National Center for Spewing Evolution will not allow that to happen without a fight.

  6. Joseph:

    Re:

    Editing and splicing require knowledge- knowledge of what is to edited/ spliced, knowledge of how to edit/ splice, knowledge of when to edit/ splice, etc.

    Excellent point. I would also add, purpose and freedom of action: the snipping and restitching targets and achieves a function, based on information as coded, and cannot be done willy-nilly. Something has to direct the snip, and has to be free to set: snip-here, stitch this then that, etc. Otherwise, you are back in the vasst sea of chaotic non-functional configs that dominate the config space.

    Can our evolutionary materialism-supporting objectors supply a counter-example?

    The Internet has billions of supportive cases in point, as do our libraries.

    Yet another sign of functionally specific, complex information and associated organisation and algorithmic processing serving as empirically reliable signs of intelligently directed configuration, AKA design.

    So, if we see editing and cut-paste functions and operations, even if automatically programmed, that is telling us yet again that something is credibly designed in the living cell.

    But, if a la Lewontin, you insist that we must not ever let anything through that just might let in a divine foot into the door . . .

    GEM of TKI

  7. . . a counter example that we directly see the origin of?

  8. How about an engineer’s foot?

    Can we allow that in the door?

    As for an exampe, you know that the only example will be living organisms- as in we see splicing and editing in living organisms so therefor no designer required. ;)

  9. Joseph:

    When we see an algorithmic, information rich process in action, the logical thing is to look for the engineer.

    You do not — at least, reasonably — infer from automatic function to nope, no designer.

    At least, without direct evidence of such FSCI rich processes spontaneously coming to be without designers and active information.

    GAs like avida and ev and weasel need not apply.

    G

  10. Actually GAs like avida, ev and weasel apply to Intelligent Design.

    But anyway we just got dumped on by about a foot of snow- any chance you would like to switch residences? :)

  11. Joseph:

    BRRR!

    You all are welcome to come join us in the Caribbean.

    And the heavy seas seem to be settling so the NA storms must be getting quiet for the moment.

    GA’s are ID but are often put up as if they were a model for unintelligent evolution. Ever since Dawkins’ Weasel rhetorical gambits in 1986 and 1987. (He admitted he knew the analogy was not apt [as in targetted, proximity-reward search . . . ], but used it anyway . . . and, sad to say, it was very persuasive and successful rhetorically. As in, “this way to the egress.” [If you went to look at what an egress was, you were outside PT Barnum;s exhibition hall, and had to pay to re-enter.)

    GEM of TKI

  12. At least, without direct evidence of such FSCI rich processes spontaneously coming to be without designers and active information.

    I wonder if it’s even possible in principle to demonstrate “FSCI rich processes coming to be without designers and active information.” That strikes me as similar to asking for a demonstration that something can, in fact, come from nothing – and also uncaused to boot.

  13. Null:

    These days, we have eminent physicists trying to tell us that we can get whole universes from nothing!

    (Cf my remarks on Hawking et al, from here on in another thread. I agree with you, but believe it or not the issue is serious. There are people who now reject the concept that that which begins or is contingent otherwise, has a cause, where cause includes necessary [blocking/enabling if absent/present] factors. In the case of Hawking et al, there is an implied substructure cosmos as a whole that has to be at a finely balanced operating point for our cosmos to exist. It was particularly rich to see Wiki give the example of virtual particle-antiparticle pairs in the quantum vacuum and then blandly announce that something came from nothing! Oops . . . [Cf. here, at point 5])

    What I am asking is quite similar, in principle to how the laws of thermodynamics are demonstrated, in particular, the second one.

    I assert X will not be observable as a spontaneous event on the gamut of the cosmos. The test, we routinely observe NOT-X, we have good statistical model based reasons for observing that X will not be plausibly observable on the gamut of the cosmos, and to date we see no cases of X arising spontaneously.

    In thermodynamics, we do not, e.g. observe heat spontaneously moving from cold to hot, and have the Clausius form: ds>/= d’Q/T

    Statistical mech tells us that the reason has to do with distributions of statistical weights of macrostates and equiprobable [per indifference] microstates, where the numbers of micro-states of distribution of matter and energy in question are astronomical.

    We observe that the rule holds, we see good reason why, and we see no counter instances to a very large number of tests. So, we can use the form that a perpetual motion machine of the second kind is impossible on the gamut of the observed cosmos.

    This is actually directly tied to the FSCI generation issue, through the statistics of large config spaces and the resulting inability of the observed cosmos as a whole to scan more than 1 in 10^150 of the config space of 1,000 bits, 1.07*10^301 states. Thus, once islands of function are deeply isolated [what "specific" implies], they will confidently be unobservable on a random walk from an arbitrary initial condition.

    An intelligence, however, is able to use insight, knowledge, information and imagination to construct an entity that is on such an island of function. Contrast writing sentences in English for a long enough post — a 20 word or so post will typically be enough — and writing the equivalent by random typing of 130 or so characters.

    These things are all connected, through Brillouin’s negentropy view of information and Maxwell’s demon (as I discuss in App 1 my always linked, on thermodynamics issues).

    Indeed the indefatigable BA77 has dug up a textbook chapter from the 70′s that anticipates much of the current discussion, here. (I would love to see his vault of treasures!)

    GEM of TKI

  14. Kairosfocus,

    I agree with you, but believe it or not the issue is serious. There are people who now reject the concept that that which begins or is contingent otherwise, has a cause, where cause includes necessary [blocking/enabling if absent/present] factors.

    Agreed. Then again, is that really new? There used to be a word for people like that. Superstitious? Irrational? Something along those lines.

    I’ve seen far, far too many people show up on here and insist that something can in fact come from nothing or events can happen without a cause. Rather did a number on my faith in the ability of most people to reason, I admit.

    We observe that the rule holds, we see good reason why, and we see no counter instances to a very large number of tests. So, we can use the form that a perpetual motion machine of the second kind is impossible on the gamut of the observed cosmos.

    Alright, but that makes me wonder about something from another angle. Let’s say – totally hypothetically – we routinely observed FCSI arising in nature. In fact, let’s say it was a downright everyday event. But it seems to me we’re still left with inferences to intelligence even in that case, because the cosmos’ ability to generate FCSI is itself going to require explanation.

    To play on a theme Joseph seemed to touch on (as did the paper he quoted), it seems that we’ve got inferences to a designer, or to engineering, screaming at us even before we start discussing FCSI. (Would that be your own view, Joseph?) That is, even if there are somehow ‘processes that generate FCSI’ we’d still be looking at something which looks incredibly like a forward-looking process, and/or a teleological one.

    Front-loading or quasi-front-loading, I suppose it’d be called. Even if intervention took place at certain points in history, the progress of history may at the same time seem to be working in preparation for those moments of intervention, to put it one way.

  15. Null:

    If the cosmos did contain FSCI-emitters, it would suggest the cosmos was programmed so to do, i.e there would be a mechanism built in that made this happen.

    But the FSCI would point to a distinction between the operating perhaps self-replicating FSCI-emitting entity, and its ultimate origin.

    And, it should be obvious where I am pointing, for the cosmos does have in it, at least on our planet, FSCI emitters: the living, metabolising, self-replicating on a code, cell.

    In that context, the issue is the origin, not the transmission of FSCI from one generation to the next. And, we see that routinely, FSCI originates in intelligence, and on grounds that random walks in sufficiently large config spaces are utterly unlikely to arrive on shores of islands of such specific function.

    I don’t know if that answers in the generic form of your point, but it speaks to the specific observable case of interest.

    GEM of TKI

  16. F/N: Null, there is of course another FSCI emitter in the physical, observable world.

    Us.

    We are not merely replicators and transmitters of FSCI, but creative, conscious originators, indeed, we are intent-ful, intelligent, knowledgeable designers. Whether of sentences or operating systems and microcontrollers.

    And that in turn raises the question of the origin of mind, and its credibility to access and understand then accurately represent and artfully refashion the world. (Notice my discussion of the Derek Smith model.)

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