Tuesday, January 13, 2015

On The Origin of Genieology - 2

Magic words: teleology
In the first post of this series I discussed the myths about human genetics that are still perpetuated by an unaware science media.

Today I want to zero in on one of the more detailed reasons why the myths persist.

I mean the usage of "magic words" on the part of science writers and/or scientists plagued with the teleology bug.

Those who have not disciplined themselves into a solid nomenclature.

More on that later in this post, after we consider a very recent scientific paper.

That recent scientific paper confirms, in part, a line of reasoning that was set forth in a hypothesis presented in the Dredd Blog series: On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12.

A day after the first post in this series was published here on Dredd Blog, a paper came out in the Journal of Theoretical Biology, authored by Dr. Meredith Root-Bernstein:
"When organic chemists anthropomorphize molecules, they say that moleculeswant to be in their lowest energy conformation”. This means that when they have energy molecules can move into different conformations, but they have a resting position that they come back to."
(The Selfish Ribosome, emphasis added). The author's use of "anthropomorphize" is a misnomer or perhaps a mistranslation:
anthropomorphize: to ascribe human form or attributes to (a ... material object ...)
(Dictionary, emphasis added). There is a proper term that has arisen for describing, more exactly, those instances when science writers and/or scientists improperly use magic words:
My interpretation of that statement is that Dr. Penrose thinks that evolutionary biologists utilize too much teleological language, and other observers agree with Penrose:
Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
(Teleological Explanations in Biology, emphasis added). The piece "Teleological Notions in Biology" adds further insight.

This teleological factor lingers in the literature even after many years have passed since "the modern synthesis":
The modern evolutionary synthesis is a 20th-century union of ideas from several biological specialties which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis and the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds. The previous development of population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(Wikipedia, emphasis added). That has led me to zero in on 1) teleology, 2) the modern synthesis, and 3) the issue of the impact of quantum mechanical concepts on evolutionary biology.
(The Uncertain Gene - 2, emphasis in original). Teleology concerns word genies and the word magic in scientific writing and/or thinking that has caused mountains of problems.

Neither genes, molecules, nor atoms want or feel, including a feeling of selfishness, because they have no self, they are abiotic molecular machines, i.e., they are not selves which are alive.

That now having been said, let's move on to the paper which has a lot of interesting merit to it:
We suggest that a ribosome-like entity was one of the key intermediaries between prebiotic and cellular evolution. Ribosomes are prerequisites to all cellular life, ubiquitously conserved, with genetic roots that pre-date LUCA, and therefore entities that had to evolve prior to cellular life itself (Mushegian, 2008; Wang et al., 2009; Fox, 2010). While the ribosome may not be capable of the broad metabolic processes that characterize cellular life, the ribosome is a self-organizing complex composed of both polynucleotides and proteins that could link RNA-world to compositional replication concepts in the origins of life. Moreover, ribosomes carry out some of the most fundamental processes characteristic of living systems, including a coordinated series of chemical reactions capable of translating genetic information into functional proteins. What ribosomes are not thought to do is to carry genetic information, and in particular the genetic information required to encode their own structures and functions. But what if ribosomal RNA (rRNA), which is generally considered to be simply a structural component of ribosomes, actually represents a primitive genome encoding the genetic information needed to direct ribosomal replication, translation and self-organization?
(Journal of Theoretical Biology, 367, (2015), pp. 130–158, at p. 131; PDF). This is the same idea I talked about in a post last year:
Today, we take a first glance into the evolution of the ribosome, which is a sophisticated molecular machine that makes and/or assembles other molecular machines, such as RNA and/or DNA, and the like (Wikipedia).

The ribosome has also been called a molecular factory that perhaps can be envisioned metaphorically by the photo to the left.

In this hypothetical look at the evolution of the ribosome (perhaps we should call its earliest manifestations a "robosome"), let's first remember one principle we talked about yesterday, which is that evolution in general is said to proceed from simple to complex.

So, let's boil this down and apply it to molecular machine evolution with this basic principle: all parts of a machine must actually exist before the complete machine itself can actually be made to exist (i.e. assembled).

Whether you are building a model car or a model airplane, or even real ones, you must first have all the parts before you can assemble those parts into a complete vehicle.

The factory in the photo at the top of this post could not assemble a complete entity, in this case an automobile, if any part was missing or did not yet exist.

That is the hypothetical model I am following to articulate how the "robosome" / ribosome must have incrementally evolved part by part, piece by piece, and simple to complex (some viruses still have molecular motors that help with genetic work -- see this).
(On the Origin of the Genes of Viruses - 4). Either molecular machines evolved or they did not.

Likewise, either cells evolved from those molecular machines or they did not.

So, let's not be afraid to discuss abiotic evolution, without teleology or teleonomy, because abiotic evolution is the big picture (Weekend Rebel Science Excursion - 27).

And, let's not make up magic words with which to construct magic ideas about "selfish" entities that cannot be selfish, because they have no self to be selfish with.

They are merely abiotic molecular machines which evolved into more complex biotic entities, or they didn't.

The next post in this series is here, the previous post in this series is here.

Dylan and Donovan ... ("let's get together and I'll turn you on to some things ...")



11 comments:

  1. Dredd, i'm not following the end statement. What do you mean "They are merely abiotic molecular machines which evolved into more complex biotic entities, or they didn't." Isn't that a tautology? In that - either something happened or it didn't - doesn't tell us anything and i don't know where to go regarding your thesis.

    Tom

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    1. Molecular machines are not selfish, lonely, horny, needy, nor properly described by any other magic words that have been used by wayward mouths in instances of teleology or teleonomy.

      The magic words are unscientific.

      The abiotic era of evolution is about 13 bn yrs. of molecular replication without self.

      And without biotic intelligence of any sort since no biology had evolved yet (e.g. Did Abiotic Intelligence Precede Biotic Intelligence?).

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    2. Tom,

      You asked:
      "They are merely abiotic molecular machines which evolved into more complex biotic entities, or they didn't."

      Isn't that a tautology?
      "
      =====================================
      It is a hypothesis that can be proven or falsified, which means it is not a tautology (In logic, a tautology ... is a formula that is true in every possible interpretation - Wikipedia).

      But the hypothesis can not be proven or falsified until the magic words are removed and a proper scientific discussion takes place concerning robosomes (molecular machines) and robozymes (molecular machines) ... which is what I tried to get going in several Dredd Blog series.

      How did abiotic entities evolve when there were no instances of primal clouds of "selfishness" or "loneliness" or "hornyness" or "neediness" (unless those were contained in the entity that went all Big Bang to form the initial abiotic realm).

      A scientific discussion is one that is not polluted with magic words such as "selfish" or "lonely" or "horny" or "needy" or any other condition injected into a place that has no such biological dynamics.

      Those we can discuss by concerning ourselves with dynamics that evolved in the biotic realm some 10-13 bn years later, such as in the relatively recent realm of mammals.

      Delete
  2. Viruses are another interesting area because they are said to be alive and not alive for about 100 years now.

    Both may be true if viruses are the bridge from the abiotic (not alive, not biological) to the biotic (alive, biological) realms (lOn the Origin of the Genes of Viruses - 3).

    And they horizontally transfer their genetic material ("If not for a virus, none of us would ever be born").

    ReplyDelete
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    1. The first sentence reads better as:

      Viruses are another interesting area, because for about 100 years now, they have been said to be both alive and not alive depending on the source.

      Recent discoveries of large viruses (e.g. as large as single celled bacteria) enhance the "they are alive" argument.

      Thus, we have an entity that still exists in abiotic forms as well as biotic forms (alive and not alive).

      That is why I think viruses should be considered as was laid out in the series "On The Origin of the Genes of Viruses" ... i.e. a bridge from the abiotic realm to the biotic realm.

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  3. The way I look at it is to consider describing the evolution of my lawn mower.

    I would likely be laughed at if I told people that it is a selfish, lonely, horny, and needy machine.

    Talking about molecules that way would be similar.

    There is a significant difference between "abiotic" and "biotic", so using the same words to describe both is uncalled for.

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  4. Got it - thanks for the explanation.

    Tom

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  5. Do viruses lurking in our genes make us smarter? Not really

    http://www.sott.net/article/291313-Do-viruses-lurking-in-our-genes-make-us-smarter-Not-really

    [quote]

    So in this study, Prof Jakobsson and his team wondered whether deleting TRIM28 might have a role to play in how neurons function by affecting expression of endogenous retroviruses.

    To test this, the researchers took neuronal progenitor cells (stem-like cells that are on their way to becoming neurons) from mice that had the TRIM28 gene deleted and cultured them in the laboratory. They found that deleting TRIM28 in neuronal progenitor cells led to an increased expression of endogenous retroviruses which then altered the expression of nearby genes on the mouse genome.

    The is is an exciting finding showing that there might be a mechanism of genetic regulation in the brain that we do not yet know about, one that is controlled by endogenous retroviruses. However, nowhere in the TRIM28 study do the researchers claim that TRIM28, endogenous retroviruses and intelligence are somehow connected. And appropriately so, considering that the study was conducted only on cultured cells and will need a lot more work to relate the finding to an effect on intelligence.

    So where did the erroneous claims in the news come from? From the press release as it turns out, which had the headline - "Do viruses make us smarter?" Even though the body of the press release itself makes no reference to intelligence, the provocative headline is catching the eyes of reporters. Unfortunately, it is also having the consequence of spreading an idea that has no scientific backing.

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    1. Anonymous,

      You asked: "Do viruses lurking in our genes make us smarter?"

      Viruses do not lurk in our genes, or in any other organism's genes, because they are much larger than any gene.

      The article you linked to says "Research stemming from the human genome project showed that there are at least 100,000 known viral fragments that are part of the human genome."

      The human genome project discovered that the human genome has at most ~25,000 genes: "Some would say that genomics has been able to distil some humility into humankind. The finalised version of the human genome deprived us of the illusion that we are one of the most complex creatures on Earth — an illusion that was at the basis of some guesses that Homo sapiens was expected to have at least 100,000 genes. When we look at a table of genomes by species, and specifically at the number of genes that have been counted or estimated for each species, we notice that humans are surpassed by several plants and invertebrates. (The Human Microbiome Congress).

      (continued below}

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    2. (continued from above)

      Genes came into existence billions of years before humans did, so linking genes with intelligence requires more discussion than how genes of viruses might impact upon human intelligence (Did Abiotic Intelligence Precede Biotic Intelligence?, cf . What Kind of Intelligence Is A Lethal Mutation?).

      But first, the nature of intelligence needs to be established, then a discussion of whether humans as members of a suicidal civilization in a premature solar system phase fit into that mold (Civilization Is Now On Suicide Watch, 2, 3, 4).

      It may be that actual intelligence in biological organisms cannot develop until the last phase of a solar system's stellar evolution is complete (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12).

      We are not there yet (ibid at 6).

      Anyway, thank you for a really interesting comment.

      Keep researching and keep sharing.

      Delete
  6. The book "Viruses: Essential Agents of Life" on Amazon, mentioned and linked to in Dredd's post "On The Origin of the Genes of Viruses" has this description of the book: "A renaissance of virus research is taking centre stage in biology. Empirical data from the last decade indicate the important roles of viruses, both in the evolution of all life and as symbionts of host organisms. There is increasing evidence that all cellular life is colonized by exogenous and/or endogenous viruses in a non-lytic but persistent lifestyle. Viruses and viral parts form the most numerous genetic matter on this planet."

    ReplyDelete