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Biology’s many surprises

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From Ann Gauger at Evolution News & Views

About forty years ago, a biochemistry professor told my class that now that the genetic code had been worked out and the lac operon discovered, the only thing left for us students was to work out the details. Boy, was he wrong!

If there’s one thing I’ve learned over the last forty years, it is that every ten years or so the biological apple cart is upset, and a long-established “fact,” an assumption based on incomplete knowledge, is proven to be wrong.

I am sure you can find textbooks that still include some of these old “facts.” Below is a partial list of those assumptions that have had to be revised, and some that are still under discussion.

1. Old fact: DNA is stable and genes don’t hop around.

New discovery: Mobile genetic elements can hop from place to place in the DNA, duplicating themselves and changing gene expression. Sometimes they carry surrounding genes with them. More.

19 Replies to “Biology’s many surprises

  1. 1
    Acartia_bogart says:

    DNA bouncing around has been known since the 60s. Hardly recent considering that extensive research on DNA and its functioned didn’t really begin until the 1950s (and before BA77 jumps in, yes, I know that the actual chemical was discovered in the late 1800s). And RNA based viruses were known long before tRNA, mRNA and rRNA were discovered. There goes another one of those “so called” surprises. And junk DNA still dominates the genome, in spite if ID’s efforts to claim otherwise.

    In short, introns are about the only recent discoveries that came as a surprise. Hardly a convincing argument for ID

  2. 2
    awstar says:

    per Wiki:

    An intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.

    So A-B, how does evolution theory explain how it came to be that a nucleotide sequence within a gene is removed by RNA splicing?

    It seems to me (unless you come up with a reasonable explanation) this would be a convincing argument for ID?

  3. 3
    Querius says:

    [sound of crickets chirping]

    Notice how darwinists, as the aristotelians before them, grip tightly to the sinking ship’s rails, in this case “junk” DNA, to the bitter end.

    -Q

  4. 4
    Dr JDD says:

    Unfortunately, posts like A_B while laced with elements of truth, massively downplay the ultimate truth to favour a proposed materialistic worldview and (as per Q) like the proud captain of a sinking ship, stands on the 2% left above water confidently declaring “this ship can still sail!”

    Many things are surprising about the genome. It is certainly surprising that there are perhaps, more regulatory RNA molecules than there are genes themselves. This is on the list. siRNA was the discovery of the year I think in 2001/2 time. lncRNA, lincRNA, and the brothers and sisters of these stretches of RNA that seemed to be heavily involved in regulation of gene expression, tissue specific expression, developmental expression and thus timing of expression are no small components of DNA. Overlapping genes, multiple frames of information layered, differential RNA products depending on the 5’ or 3’ direction of transcription…all of these things are quite recent findings, and certainly very surprising from a materialistic standpoint.

    Further, the epigenetics that takes place at the level of the genome is vastly surprising. Certainly just the complexity of histone and DNA packaging is a marvel itself, but then considering the vast array of various modifications not just to DNA but also to histones (methylation being the best studied example, but there are many more) that serve to imprint environmental changes to a hereditary function on the gene but also silence and regulate and activate gene expression, sometimes in different ways depending on the different histone molecule, for example in histone modifications. Further to this, it is not simply the case of a single methyl group addition turning on or off a gene area on histone modification, but rather di- and tri-methylation states all differing in how the genome responds to such modification.

    No, these are certainly not expected complexities given the model of “natural selection through the mechanism of random mutation drives upwards complexity” and as such complexities are observed throughout all of life itself, we are certainly left with many surprises if we were to view such processes from a naturalistic point of view (as modern science apparently demands us to do).

    However some might like to take alternative views, outside of the realm of what ID specifically addresses:

    “When I consider…the works of your fingertips…what is man that you are mindful of him, the son of man that you care for him?”

    “Who has put wisdom in the innermost being or given understanding to the mind?”

    “Great are the works of the LORD, they are studied by all who delight in Him.”

    “I am fearfully and wonderfully made; wonderful are Your works and my soul knows it very well.”

  5. 5
    wd400 says:

    No, these are certainly not expected complexities given the model of “natural selection through the mechanism of random mutation drives upwards complexity” and as such complexities are observed throughout all of life itself,

    H’uh? If NS led to complexity (there is no reason it needs to) why would complexity be limited to some groups and not others? Did some groups opt out of natural selection?

    (In fact, we do know selection is a stronger force in some lineages that others, and there is a pretty good negative correlation between selective force and the messiness of genomes so…)

  6. 6
    bornagain77 says:

    wd400, to the extent that Natural Selection does do anything, Natural Selection is found to be a eliminative force not a generative force:

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED – Natural Selection And Genetic Mutations – video
    https://www.youtube.com/watch?v=6z5-15wk1Zk

    From a Frog to a Prince – video (17:00 minute mark Natural Selection Reduces Genetic Information) – No Beneficial Mutations – Gitt – Spetner – Denton – video
    https://www.youtube.com/watch?v=ClleN8ysimg&feature=player_detailpage#t=1031

    “A Dutch zoologist, J.J. Duyvene de Wit, clearly demonstrated that the process of speciation (such as the appearance of many varieties of dogs and cats) is inevitably bound up with genetic depletion as a result of natural selection. When this scientifically established fact is applied to the question of whether man could have evolved from ape-like animals,’.. the transformist concept of progressive evolution is pierced in its very vitals.’ The reason for this, J.J. Duyvene de Wit went on to explain, is that the whole process of evolution from animal to man ” ‘ . . would have to run against the gradient of genetic depletion. That is to say, . . man )should possess] a smaller gene-potential than his animal ancestors! [I] Here, the impressive absurdity becomes clear in which the transformist doctrine [the theory of evolution] entangles itself when, in flat contradiction to the factual scientific evidence, it dogmatically asserts that man has evolved from the animal kingdom!” —Op. cit., pp. 129-130. [Italics his; quotations from *J.J. Duyvene de Wit, A New Critique of the Transformist Principle in Evolutionary Biology (1965), p. 56,57.]
    http://www.godrules.net/evolut.....vlch15.htm

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.”
    Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    It is not that hard to learn why Natural selection is a eliminative force instead of a generative force. Simply put, if evolution were actually the truth about how all life came to be on Earth then the only ‘life’ that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the ‘fittest’ are allowed to survive. The logic of all this is nicely summed up here:

    Richard Dawkins interview with a ‘Darwinian’ physician goes off track – video
    Excerpt: “I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly — a few hours sometimes, they can reproduce themselves — that they can evolve very, very quickly. And we’re stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?”
    http://www.evolutionnews.org/2.....62031.html

    i.e. Since successful reproduction is all that really matters on a neo-Darwinian view of things, how can anything but successful reproduction be realistically ‘selected’ for? Any other function besides reproduction, such as sight, hearing, thinking, etc.., would be highly superfluous to the primary criteria of successfully reproducing, and should, on a Darwinian view, be discarded as so much excess baggage since it would slow down successful reproduction.

    As well, Natural Selection is grossly inadequate to do the work required of it because of what is termed ‘the princess and the pea’ paradox. The devastating ‘princess and the pea’ paradox is clearly elucidated by Dr. John Sanford, at the 8:14 minute mark, of this following video,,,

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video
    http://vimeo.com/35088933

    Dr. Sanford points out, in the preceding video, that Natural Selection acts at the coarse level of the entire organism (phenotype) and yet the vast majority of mutations have effects that are only ‘slightly detrimental’, and have no noticeable effect on phenotypes, and are thus far below the power of Natural Selection to remove from genomes before they spread throughout the population.

    “Selection Threshold Severely Constrains Capture of Beneficial Mutations” – John Sanford – September 6, 2013
    Excerpt of concluding comments: Our findings raise a very interesting theoretical problem — in a large genome, how do the millions of low-impact (yet functional) nucleotides arise? It is universally agreed that selection works very well for high-impact mutations. However, unless some new and as yet undiscovered process is operating in nature, there should be selection breakdown for the great majority of mutations that have small impact on fitness.,,,
    We show that selection breakdown is not just a simple function of population size, but is seriously impacted by other factors, especially selection interference. We are convinced that our formulation and methodology (i.e., genetic accounting) provide the most biologically-realistic analysis of selection breakdown to date.
    http://www.worldscientific.com.....08728_0011

  7. 7
    bornagain77 says:

    Here are a few more notes on this insurmountable ‘princess and the pea’ problem for natural selection:

    Evolution vs. Genetic Entropy – Andy McIntosh – video
    https://vimeo.com/91162565

    The GS Principle (The Genetic Selection Principle) – Abel – 2009
    Excerpt: The GS Principle, sometimes called “The 2nd Law of Biology,” states that selection must occur at the molecular/genetic level, not just at the fittest phenotypic/organismic level, to produce and explain life.,,, Natural selection cannot operate at the genetic level.
    http://www.bioscience.org/2009.....lltext.htm

    Moreover, as if that were not devastating enough as to undermining any credibility Natural Selection might have had as to having the causal adequacy to explain the highly integrated levels of overlapping functional information found in organisms, dimensionally speaking, Natural Selection is now known to not even be on the right playing field in the first place:

    The predominance of quarter-power (4-D) scaling in biology
    Excerpt: Many fundamental characteristics of organisms scale
    with body size as power laws of the form:

    Y = Yo M^b,

    where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent.
    A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling.
    http://www.nceas.ucsb.edu/~dre.....18_257.pdf

    “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79

    Here is, what a Darwinist termed, a ‘horrendously complex’ metabolic pathway (which operates as if it were ’4-Dimensional):

    ExPASy – Biochemical Pathways – interactive schematic
    http://web.expasy.org/cgi-bin/.....mbnails.pl

    And remember, Darwinian evolution has yet to explain a single gene of those ‘horrendously complex’ metabolic pathways.

    “Charles Darwin said (paraphrase), ‘If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.’ Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It’s a mirage. None of it happens that way.
    – Doug Axe PhD. – Nothing In Molecular Biology Is Gradual – video
    http://www.metacafe.com/watch/5347797/

    The reason why a ‘higher dimensional’ 4-Dimensional structure, such as a ‘horrendously complex metabolic pathway, would be, for all intents and purposes, completely invisible to a 3-Dimensional process, such as Natural Selection, is best illustrated by ‘flatland’:

    Flatland – 3D to 4D shift – Dr. Quantum – video
    http://www.youtube.com/watch?v=BWyTxCsIXE4

    I personally hold that the reason why internal physiology and anatomy operate as if they were four-dimensional instead of three dimensional is because of exactly what Darwinian evolution has consistently failed to explain the origination of. i.e. functional information. ‘Higher dimensional’ information, which is bursting at the seams in life, simply cannot be reduced to any 3-dimensional energy-matter basis:

    John Lennox – Is There Evidence of Something Beyond Nature? (Semiotic Information) – video
    http://www.youtube.com/watch?v=F6rd4HEdffw

    “One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin?
    And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce.
    In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires.
    Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.”
    -Dr. Stephen C. Meyer earned his Ph.D. in the History and Philosophy of science from Cambridge University for a dissertation on the history of origin-of-life biology and the methodology of the historical sciences.

  8. 8
    Dr JDD says:

    If NS led to complexity (there is no reason it needs to) why would complexity be limited to some groups and not others? Did some groups opt out of natural selection?

    But it does, surely. Considering we started apparently but with a handful of simple genes and now have 1000s along with other regulatory events, and the overriding mechanism to select from the simple to the complex therefore is tauted to be NS therefore through NS as a mechanism upwards complexity is achieved, according to the naturalistic theory.

    Secondly, why would we not see remnants of more simple organisms? Why are the simplest organisms quite complex? Why, if such simpler organisms still survive and live and do not die out (those that we supposedly evolved from) is the argument that they went on evolving more complex but there are no remnants of the simpler ones, closer to abiogenesis? If royal ferns do not undergo evolution for 500million years, if other organisms are found to not change in such large time-scales, why would we expect the more simpler versions of our current simplest organisms to not be present?

    But this, like many arguments of evolutionists (as this is used as an argument FOR evolution – i.e. we see complexity in simpler organisms because they have evolved), is a non-argument for evolution. Why? Because if the converse was observed, it would also be used as evidence for evolution. I.e. if we found something much simpler that shows potential for a life-like organism, some simple replication machinery that is very basic, it would be thrown up as the god of abiogenesis and proof of naturalism. We are to believe that the genetic code was different and not always a triplet. We are to believe that all that was lost yet one universal code remains. In fact, it would make more sense if naturalism was true for there to be evidence of multiple codes (not perceived predicted evidence, but actual observable evidence).

    In your final comment of “messiness of genome” you are perhaps making a large assumption of “size” of a genome being the same as “messiness” which is a pure assumption.

  9. 9
    wd400 says:

    There is no reason tat natural selection need to drive toward higher complexity over all. All that’s required is that some lineages get more complex, be that by selection or the accumulation clutter.

    Anyway, you seem to be saying something different in this comment than the last one. Why can’t selection explain, say, the presence of introns or packaging of genomes by histones? IF that’s not what you are saying what does this mean?

    No, these are certainly not expected complexities given the model of “natural selection through the mechanism of random mutation drives upwards complexity” and as such complexities are observed throughout all of life itself,

  10. 10
    Acartia_bogart says:

    Awstar: “It seems to me (unless you come up with a reasonable explanation) this would be a convincing argument for ID?”

    I don’t follow the logic. Because I can’t explain it, it must be intelligent design? I don’t understand nuclear fusion, or Italian either. But I am pretty confident that they are not the result of magic.

  11. 11
    Dr JDD says:

    I never said that natural selection per se HAS to drive towards higher complexity. But as what we see it complexity and we are told we were once simpler, therefore NS must have resulted in increased complexity. I do not understand why you seem to take issue with this basic complex. Nowhere have I said the mechanism of NS requires an increase in complexity.

    The argument is:
    1) NS selection is the mechanistic driving force behind evolution
    2) We observe complexity in life today
    3) Life must have been much simpler in the past
    4) Therefore, NS has driven simplicity to complexity

    There is not the need for NS to do so, but it has, if you accept the evolutionary tale.

    Secondly, NS acts upon the genetic information and the code through mutation. Yet this mechanism is out of reach of the complexities of things like histone modification and epigenetic control. However evolutionists just hand-wave, throw the arbitrary argument about millions and billions of years (implying near infinity for chance to do its work) without providing any good reason why it can explain these complexities we see beyond the straightforward genetic code. When something is outside of that mechanism, the onus is on the person claiming that mechanism can also account for those properties as well, rather than the onus on someone questioning that to prove it cannot account for it.

    However the standard “shut-them-up” evolutionary answer is something along the lines of “we all know in the case of methyl groups that they require a methyltransferase so simply a methyltransferase evolved and happened to modify DNA and that happened to provide control.” It is an illogical argument to say that something that regulates the very mechanism that allows expression of a positive attribute arose from that same attribute. One I completely reject as based on good science.

  12. 12
    wd400 says:

    I’m asking a very simple question, which you have yet to answer. What does this mean? Especially the all throughout life bit?

    No, these are certainly not expected complexities given the model of “natural selection through the mechanism of random mutation drives upwards complexity” and as such complexities are observed throughout all of life itself,

  13. 13
    wd400 says:

    (that is, a simple reading of your statement seems to imply that the fact “complex” features are widespread in the tree of life means selection can’t explain them. I don’t get the argument, so am asking you to clarify)

  14. 14
    ppolish says:

    Darwin’s final sentence in The Origin of Species starts off with:

    “There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one;”

    What did Darwin mean by:
    1) Several Powers
    2) Breathed by the Creator
    3) Few Forms or unto One

  15. 15
    wd400 says:

    1) The several powers are laws of growth, reproduction, variation, selection and on described in the preceding paragraph.

    2) That’s god and reference to genesis (though the creator only appears in later issues)

    3) All life descends from one or a few ancestors [turns out it’s one]

    Why do you ask?

  16. 16
    ppolish says:

    Wd400, as a Theistic ID’er I also believe in several powers breathed by the Creator into a few forms(Cambrian eg) and/or one(OOL).

    I ask because I’m afraid I might be a Darwinist. Maybe that explains my Darwinphobia yikes.

  17. 17
    bornagain77 says:

    as to:

    “(though the creator only appears in later issues)”

    Actually, ‘Origin’ is rife with, and dependent on, faulty theological premises from its earliest editions onwards:

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    Excerpt: The Origin supplies abundant evidence of theology in action; as Dilley observes:
    I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation):

    1. Human begins are not justfied in believing that God creates in ways analogous to the intellectual powers of the human mind.
    2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern.
    3. A respectable deity would create biological structures in accord with a human conception of the ‘simplest mode’ to accomplish the functions of these structures.
    4. God would only create the minimum structure required for a given part’s function.
    5. God does not provide false empirical information about the origins of organisms.
    6. God impressed the laws of nature on matter.
    7. God directly created the first ‘primordial’ life.
    8. God did not perform miracles within organic history subsequent to the creation of the first life.
    9. A ‘distant’ God is not morally culpable for natural pain and suffering.
    10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering.
    http://www.evolutionnews.org/2.....46391.html

    The Descent of Darwin – Pastor Joe Boot – (The Theodicy of Darwinism) – article
    http://www.ezrainstitute.ca/ez.....spring.pdf

    Since Darwin’s book ‘Origin of Species’, besides being bad science, is also rife with bad theology, it is not that surprising that liberal clergy have been very eager to jump on the Darwinian bandwagon from the beginning:

    “Religious views were mixed, with the Church of England scientific establishment reacting against the book, while liberal Anglicans strongly supported Darwin’s natural selection as an instrument of God’s design.”
    http://en.wikipedia.org/wiki/R.....of_Species

  18. 18
    bornagain77 says:

    as to:

    All life descends from one or a few ancestors [turns out it’s one]

    that claim, as with much of what wd400 says, is just plain false.

  19. 19
    ppolish says:

    All life descending from one is much more fantastical than all Human life descending from two.

    Wd400, do you believe One Life happened in a specific place on Earth at a given time? Or maybe all over the place at about the same time. Maybe even different kinds of One Life in many different places at about the same time.

    Seriously, you believe in One Life in one
    place. And all subsequent life came from that little dude/dudette?

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