Charles Clanton Rogers

Reflections based on poetry, music, visual art, book reviews, history of science, first-person history, philosophical essays and International Blogging

https://clanton1934.files.wordpress.com/2015/07/46-prelude-a-lapres-midi-dun-faune.m4aiStock_000016452192_Full

On August 5, 2015, I published a blog post, “Life Is Inexplicable”, reviewing contrasting views on the origin of life (Addy Proos and Richard Dawson).   I received a lot of interest in that post. The link to that post is:

http://therogerspost.com/2015/08/05/life-inexplicable/

My discussions in “Life Is A Journey” further discussed these questions; see this link

http://therogerspost.com/2015/08/16/life-process/

My opinion remains contrary to the random-mechanism scientists, (Dawkins and Hoffman), (9, 12) who believe life rose by only random, physical encounters of, first, organic chemicals, then “living molecules”. These scientist believe that living DNA replicates itself,  and all life by random mistakes without a purpose. I concluded that in spite of remarkable findings in nano technology, I believe a mystery remains. This mystery is: from where does Dr. Proos’ “engine” came?  What continues to drive “the engine in the car” (the living cell) uphill against Newton’s  Second Law of Motion. Furthermore what has sustained this mysterious force for several billion years? (2)

Now David Bugen reports new genetic studies yielding findings that have accentuated my questions. (1)

For most of the last 40 years, scientists thought that the primary way new genes were born — was that they just arose from copies of existing genes. The old version went on doing its job, and the new copy became free to evolve novel functions.

David Begun reports: “Certain genes, however, seem to defy that origin story. They have no known relatives, and they bear no resemblance to any other gene. They’re the molecular equivalent of a mysterious beast discovered in the depths of a remote rainforest, a biological enigma seemingly unrelated to anything else on earth.”

The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of so-called junk DNA, or non-coding DNA, the mysterious stretches of DNA between genes. “Genetic function somehow springs into existence,” – David Begun (1))

Begub coins the term: “Promiscuous proteins”,  “De novo genes are also part of a larger shift, a change in our conception of what proteins look like and how they work. De novo genes are often short, and they produce small proteins. Rather than folding into a precise structure — the conventional notion of how a protein behaves — de novo proteins have a more disordered architecture. That makes them a bit floppy, allowing the protein to bind to a broader array of molecules. In biochemistry parlance, these young proteins are promiscuous.”

Begun continues: “Scientists don’t yet know a lot about how these shorter proteins behave, primarily because standard screening technologies tend to ignore them. Most methods for detecting genes and their corresponding proteins pick out long sequences with some similarity to existing genes. It’s easy to miss these,”

“That’s starting to change. As scientists recognize the importance of shorter proteins, they are implementing new gene discovery technologies. As a result, the number of de novo genes might explode. We don’t know what things shorter genes do,” Masel said. “We have a lot to learn about their role in biology.”

The questions and unknowns that I raised in “Life I Still Inexplicable” are even greater in light of the genetic findings reported by Begun. 

Scientists also want to understand how “de novo genes get incorporated into the complicated network of reactions that drive the cell, a puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. The question is fascinating but entirely unknown,”(1)

“A human-specific gene called ESRG illustrates this mystery particularly well. Some of the sequences are found in monkeys and other primates. But it is only active in humans, where it is essential for maintaining the earliest embryonic stem cells. And yet monkeys and chimps are perfectly good at making embryonic stem cells without it. “It’s a human-specific gene performing a function that must predate the gene because other organisms have these stem cells as well,” McLysaght said.

“How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”

In my opinion, Life is even more inexplicable in light of  “promiscuous proteins” and “Orphan Genes”.

Thank you for “flying Zebra!”    If you liked this post, consider hitting my reblog button or Facebook Share.

Charles Clanton Rogers, MD, FACR, Emeritus Professor, GWU   September 1, 2015

(1) Emily Singer and Skip Sterling,  A Surprise Source of Life’s Code Emerging data suggests the seemingly impossible — that mysterious new genes arise from “junk” DNA Quanta Magazine | reported in The Scientific American,  August 31, 2015

(2) Pross, Addy, What is Life,? : How Chemistry Becomes Biology. Oxford University Press. 2012

(3) Hal Hellman, Special to The Washington Post, September 9, 1998; Page H01

(4) Giorgio de Santillana, The Crime of Galileo

(5) http://www.biography.com/people/isaac-newton-9422656

(6) Norman, Andrew, Charles Darwin,: Destroyer of Myths

(7) Isaacson, Walter, Einstein,: His Life and Universe

(8) Andrew Berry and James WatsonWatson, DNA

(9) Dawkins, Richard, The Selfish Gene 30th Anniversary Edition

(10) Yuval Noah Harari, Sapiens,: A BRIEF HISTORY OF HUMANKIND, HarperCollins, 443 pages, 2014

(11) Fred Hoyle, the well-known astronomer, the likelihood of such an event would be similar to that of a whirlwind blowing through a junkyard and assembling a Boeing 747. Life’s organized complexity is strange, very strange. And how it came about is even stranger. Cited by Pross (1)

(12) Hoffmann, Peter M.. Life’s Ratchet: How Molecular Machines Extract Order from ChaosPerseus Books Group, , Philadelphia(Kindle ). Basic Books. Kindle Edition.”When we try to define life, we run into difficulties, There seems to be something indefinable, some particular ingredient that separates inanimate mater from living flesh… ‘life force.”

10 thoughts on “Life Is Even More Inexplicable – New Findings – 2015/09/01

  1. bbnewsab says:

    Very interesting thoughts, clanton1934.

    But for once I disagree with you.

    1) Have a look at https://en.wikipedia.org/wiki/Junkyard_tornado .

    A quote from that article: The junkyard tornado argument is rejected by evolutionary biologists,[3] since, as the late John Maynard Smith pointed out, “no biologist imagines that complex structures arise in a single step.”[7] The modern evolutionary synthesis explains how complex cellular structures evolved by analysing the intermediate steps required for precellular life. It is these intermediate steps that are omitted in creationist arguments, which is the cause of their overestimating of the improbability of the entire process.[1]

    Hoyle’s argument is a mainstay of creationist, intelligent design, orthogenetic and other criticisms of evolution. It has been labeled a fallacy by Richard Dawkins in his two books The Blind Watchmaker and Climbing Mount Improbable.[1] Dawkins argues that the existence of God, who under theistic uses of Hoyle’s argument is implicitly responsible for the origin of life, defies probability far more than does the spontaneous origin of life even given Hoyle’s assumptions, with Dawkins detailing his counter-argument in The God Delusion, describing God as the Ultimate Boeing 747 gambit.

    2) Also have a look at: http://molecularevolutionforum.blogspot.se/2012/05/how-can-there-be-orphan-genes.html . In that article different explanations of the orphan gene(s) phenomenon are discussed.

    3) And finally, have a look at: https://en.wikipedia.org/wiki/Orphan_gene .

    Two quotes from that Wikipedia article:

    3.A: Where do orphan genes come from?

    According to the Carvunis Model,[15] novel orphan genes continually arise from “random”, non-coding sequence. These novel genes may be sufficiently beneficial to be swept to fixation by selection. Or more likely, they will fade back into the non-genic background. That young genes are more likely to go extinct (become pseudogenes) has recently been confirmed in Drosophila .[16]

    3.B: Protein characteristics

    Orphans genes tend to be very short (~6 times shorter than mature genes), weakly expressed, tissue specific and simple in codon usage and amino acid composition.[17] Orphan genes are encoded mostly intrinsically disordered proteins.[18]

    The concept of orphan genes – the term is a misnomer, probably emanating from some God believing scientists – reminds me of many other God of the gaps explanations that creationists like to cling to.

    From the ICR (Institute for Creation Research) many articles have been published stating that the concept of orphan genes validates the creation story in Genesis and invalidate the evolution theory. See for instance: http://www.icr.org/article/newly-discovered-orphan-genes-defy/ .

    BTW, did you know, Kung Karl, that members of the ICR must take an annual oath promising that everything they publish must be in accordance with the literal interpretation of Genesis? *time for a facepalm here; or mayne more*

    Is that the way science should be done? Has God decided that? I just wonder how they motivate this oath taking procedure at the ICR.

    Anyhow, it’s kind of hard for me to believe that the ICR writers are always playing with open cards.

    Read more about the oath taking procedure here: http://rosarubicondior.blogspot.se/2015/08/creationist-lie-about-jesus.html .

    Let me finish my comment with this long quote from Rosa Rubicondior’s article:

    Members of the ICR, anyone who writes for them, and all employees are required to take an annual oath that they will never publish anything that isn’t in full accord with a literal interpretation of Genesis.

    Part of this oath deal with the ‘Tenets of Biblical Creationism’:

    TENETS OF BIBLICAL CREATIONISM

    The Creator of the universe is a triune God — Father, Son, and Holy Spirit. There is only one eternal and transcendent God, the source of all being and meaning, and He exists in three Persons, each of whom participated in the work of creation.

    The Bible, consisting of the thirty-nine canonical books of the Old Testament and the twenty-seven canonical books of the New Testament, is the divinely-inspired revelation of the Creator to man. Its unique, plenary, verbal inspiration guarantees that these writings, as originally and miraculously given, are infallible and completely authoritative on all matters with which they deal, free from error of any sort, scientific and historical as well as moral and theological.

    All things in the universe were created and made by God in the six literal days of creation week described in Genesis 1:1-2:3, and confirmed in Exodus 20:8-11. The creation record is factual, historical, and perspicuous; thus all theories of origins or development which involve evolution in any form are false. All things which now exist are sustained and ordered by God’s providential care. However, a part of the spiritual creation, Satan and his angels, rebelled against God after the creation and are attempting to thwart His divine purposes in creation.

    The first human beings, Adam and Eve, were specially created by God, and all other men and women are their descendants. In Adam, mankind was instructed to exercise “dominion” over all other created organisms, and over the earth itself (an implicit commission for true science, technology, commerce, fine art, and education) but the temptation by Satan and the entrance of sin brought God’s curse on that dominion and on mankind, culminating in death and separation from God as the natural and proper consequence.

    The Biblical record of primeval earth history in Genesis 1-11 is fully historical and perspicuous, including the creation and fall of man, the curse on the creation and its subjection to the bondage of decay, the promised Redeemer, the worldwide cataclysmic deluge in the days of Noah, the post-diluvian renewal of man’s commission to subdue the earth (now augmented by the institution of human government) and the origin of nations and languages at the tower of Babel.

    The alienation of man from his Creator because of sin can only be remedied by the Creator Himself, who became man in the person of the Lord Jesus Christ, through miraculous conception and virgin birth. In Christ were indissolubly united perfect sinless humanity and full deity, so that His substitutionary death is the only necessary and sufficient price of man’s redemption. That the redemption was completely efficacious is assured by His bodily resurrection from the dead and ascension into heaven; the resurrection of Christ is thus the focal point of history, assuring the consummation of God’s purpose in creation.

    The final restoration of creation’s perfection is yet future, but individuals can immediately be restored to fellowship with their Creator, on the basis of His redemptive work on their behalf, receiving forgiveness and eternal life solely through personal trust in the Lord Jesus Christ, accepting Him not only as estranged Creator but also as reconciling Redeemer and coming King. Those who reject Him, however, or who neglect to believe on Him, thereby continue in their state of rebellion and must ultimately be consigned to the everlasting fire prepared for the devil and his angels.

    Source: HolySmoke.

    Like

    1. clanton1934 says:

      I am very pleased with your extensive and scholarly response. At last , we have having an exchange of various views.
      I will need a day to read your references and digest the information.
      I want everyone would might be witnessing our conversations understand. None of my arguments were meant to support “Creationists”, especially such views of “young earth” and dinosaurs and humans living together like Barney Rubble! Agnostic is more nearly atheist than Creationist.
      My position is, after a half Century of science, one of stunned bewilderment. None of the great minds (e.g. Hoffman & nanotechnology) have explained “the force” even if one buys the mechanism.
      My word for my several articles is Inexplicable! The word: Inexplicable does not permit a jump to “God”!
      My dear bbnewsab, I hope this will make you laugh!!
      I just googled “Inexplicabl” (try it) — The first up citations were from articles published by me, including today’s with reproduction of my embryo image! Ha! I’m the Google example for inexplicable! Ha! Ha!
      I love that you disagreed and that we are discussing the points raised. (I still feel like the blind men describing the elephant).
      Now, give me a day to digest the references which you have served up. My very best wishes, Karl

      Liked by 1 person

  2. bbnewsab says:

    Dear Kung Karl, I think much of our disagreement can be boiied down to a semantic discord. Your post was entitled “Life Is Even More Inexplicable – New Findings”.

    That’s a wording worthy of a creationist.

    Inexplicable is an adjective I myself would never use, because I regard that word as unscientific. In my eyes It belongs to the religious language sphere.

    Science, as you well know, Karl, is about probabilities, not necessarily absolute truths (like in religions). In religions all fundamental questions are solved, even though the answers often can be difficult to find or understand (so even religious dogmas are changed over time).

    Whereas, In the scientific world, a non-divine explanation (theory) “rules” until it’s overthrown by an even better hypothesis or theory. It’s like in the world of evolution: the alpha male rules the wolf pack until he is challenged and defeated by another male and thereafter replaced by him.

    Life has made me prejudiced in some way. For example, IF a statement is used by creationists to strengthen their creed or faith, then I think that statement must be wrong.

    This prejudice of mine is based on strong statistical data. The religious standpoint has, historically speaking, a disastrous reputation. It’s full of more or less shameful and enforced retreats.

    In fact I know of no scientific problem/question whatsoever there religion has shown that the religious explanation is the right one.

    That’s why I find it very reasonable to suppose, as a premise, that the religious answer to a posed scientific question can’t be the final solution of (or right answer to) the problem in question.

    And that’s also why I questioned your use of the adjective “inexplicable” (= impossible to answer or explain).

    Life is full of wonders. Look, for instance, this video of a massive murmuration of starlings, https://www.youtube.com/watch?v=btC2OmiSR0s . All those starlings acting as if they were one orchestrated body. But yet, I wouldn’t call it “inexplicable”. Even though human air plane pilots don’t even come close to perform such “acts” with their high tech aeroplanes.

    BTW, during the night this news article reached my mail box: http://www.abc.net.au/science/articles/2015/08/31/4292949.htm .

    I’m sure you to will like that article, Karl.

    A very good morning to you, my dear cyber friend! // BB

    Like

  3. bbnewsab says:

    Reblogged this on Mass Delusions a.k.a. Magical & Religious Woo-Bullshit Thinking and commented:
    My highly valued cyber friend Charles Rogers is a very interesting blogger. He combines both knowledge and wisdom.

    In this specific blog he and I discuss/debate questions about (the genetic and evolutionary aspects of) life, especially its still unknown, at least partly, origin.

    I hope our debate will be of great interest for my blog followers, too.

    The topics discussed and penetrated also show that religion and science will never meet and probably can’t be reconciled with each other.

    For safety’s sake I feel a need to clarify that Charles Rogers -a.k.a. the blogger clanton1934 – is NOT a creationist. We both belong to the scientific “team”. So, please, don’t jump to any premature conclusions.

    Instead, start your own quest for the “truth” by reading and pondering – BOTH the blog post AND the comments.

    Liked by 1 person

  4. bbnewsab says:

    The other day you told a joke about two lumberjacks out in the middle of nowhere and how they suddenly one morning after a night’s sleep in their tent noticed a bear looking at them with hungry eyes. And how the two friends chose two different strategies to avoid becoming a good meal for the hungry beast.

    I found that story very amusing. I’ve told the same story to some friends of mine. They, too, found the joke both funny and clever.

    But earlier today I read an article about laughing syncope; see: http://mindhacks.com/2009/09/09/laughing-into-unconsciousness/ .

    I must therefore admonish you, dear Karl, to also issue a warning label included in your your blog post the next time you’re going to tell another funny joke.

    Perhaps you should also issue a disclaimer that it’s at their own risk your blog readers take part of your jokes.

    You see, I don’t want you to get sued for causing unconsciousness among readers prone to laughing syncope. :o)

    Liked by 1 person

  5. bbnewsab says:

    Talking of bears, here’s my favorite verses in the Holy Scripture (taken from 2 Kings 2:23-24 King James Version, KJV):

    23 And [the prophet Elisha] went up from thence unto Bethel: and as he was going up by the way, there came forth little children out of the city, and mocked him, and said unto him, Go up, thou bald head; go up, thou bald head.

    24 And he turned back, and looked on them, and cursed them in the name of the Lord. And there came forth two she bears out of the wood, and tare forty and two children of them.

    Every time I read those verses I feel in my atheist brain that never ever will I worship such a God.

    Not even if this God was real and not only an imaginary friend like Santa Claus.

    Rather I’d prefer Hell. (But I don’t believe in Hell either, so it’s all one to me.)

    Liked by 1 person

    1. clanton1934 says:

      Your are not to take those hand-me-down tales for more than some ancient fire side, camping stories – nightmares. see Hararai and “the Origin of Satan” by Elain Pagels

      Liked by 1 person

      1. bbnewsab says:

        I myself use to call the Bible, especially the Old Testament, fairytales for adults.

        Some adults (still) believe in Santa Claus, so why wouldn’t others choose to believe in angels, demons and gods?

        You don’t believe me? Then have a look at http://paranormal.about.com/od/othermiracles/a/Santa-Claus-Sightings.htm .

        Mundus vult decipi.

        That’s why some of us meet God (Jesus) and others Santa Claus.

        Enough said.

        Like

  6. bbnewsab says:

    I often call Kung Karl (clanton1934) a wise man, full of both knowledge and wisdom.

    Here’s a quote from one of the private emails my cyber friend Kung Karl has sent to my mailbox lately:

    Karl wrote:

    It is an old but trusted saying, and one that’s often thought, when you become a teacher [father], by your pupils, you’ll be taught.” Oscar Hamerstein

    And Karl continued: I tried to be mostly Science until my sons instructed me that Art is greater than Science. From the Caves at Lascaux > 20,000 years ago, before agriculture, before writing, before law, long before the Church and 20,000 years before Galileo, humankind-the-artist, left his message: I Am! Music, images, poetry inspires our dreams for the future and leaves our best footprints.

    Without Karl’s permission I now feel an urge to spread his wisdom words/message to all of his followers.

    Here’s my own comment to these thoughts: I prefer believing in Karl rather than in God. In Karl I trust (but not in God).

    Like

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