Article on latest OOL theory criticized for design language

_{Denyse O'Leary

April 27, 2015

Intelligent Design, News, Origin Of Life}

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Life emerged so long ago that even the rock formations covering the planet at that time have been destroyed — and with them, most chemical and geological clues to early evolution. “There’s a huge chasm between the origins of life and the last common ancestor,” said Eric Gaucher, a biologist at the Georgia Institute of Technology in Atlanta.

The stretch of time between the origins of life and the last universal common ancestor saw a series of remarkable innovations — the origins of cells, metabolism and the genetic code. But scientists know little about when they happened or the order in which they occurred.

Scientists do know that at some point in that time span, living creatures began using a genetic code, a blueprint for making complex proteins. It is those proteins that carry out the vital functions of the cell. (The structure of DNA and RNA also enables genetic information to be replicated and passed on from generation to generation, but that’s a separate process from the creation of proteins.) The components of the code and the molecular machinery that assembles them “are some of the oldest and most universal aspects of cells, and biologists are very interested in understanding the mechanisms by which they evolved,” said Paul Higgs, a biophysicist at McMaster University in Hamilton, Ontario.

According to the theory discussed in th article, the amino acid tryptophan came last.

A Quanta reader wrote to them to point out that the author uses much too colourful language, language that implies that evolution has intelligence or a goal. For example: “It then grew in complexity over time, as these proteins learned to make more sophisticated molecules.” Proteins learn? Are these newer structures “more sophisticated” (implying intelligence) or merely more complex?

Humph. Playing our song and not crediting us.

Also, Paul Schimmel, quoted in the article: “It speaks to the refinement and subtlety that nature was using to perfect these proteins and the diversity it needed to form this vast tree of life.”

Nature isn’t suppose to be a person, but in any event, it is not clear any more that there even is a tree of life

If author Emily Singer gets it on the ear from naturalists, it’s too bad. Especially when one considers that they have got hardly anywhere at all with the origin of life problem, except for all the fascinating ideas.

Which are fun, to be sure—but not quite the same thing as scientific progress.

See also: With Enceladus the toast of the solar system, here’s a wrap-up of the origin-of-life problem

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Comments

'If author Emily Singer gets it on the ear from naturalists, it’s too bad. Especially when one considers that they have got hardly anywhere at all with the origin of life problem, except for all the fascinating ideas. Which are fun, to be sure—but not quite the same thing as scientific progress.' And that, leaving aside the farcical belief in the configuration of living creatures of the most sophisticated designs, at that, having been produced in a wholly random, unguided way. Life, itself, only makes their problem four-dimensional - the last of which is understandably, if ultimately, fatuously, left entirely out of consideration.Axel_{April 29, 2015
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Of related note: How Cells Keep Right-Handed Amino Acids Out - April 29, 2015 Excerpt: One of the wonders of life at the molecular scale -- a fact that defies chance -- is the purity of left-handed amino acids in proteins. Without this "homochirality," as it is known, proteins would never fold properly into the functional structures that make life possible. Theoretically, life could be built backwards, using only right-handed amino acids -- as long as the mixture is pure. But the cell's translation machinery (TM) would have to be redesigned to accommodate the change. (Note: left-handed amino acids are prefixed by L- and right-handed ones by D-). Whenever amino acids form naturally, they occur in "racemic" mixtures of L- and D- "isoforms." It's been a long-standing mystery in the origin-of-life community how cells first discriminated between them. The physical and thermodynamic properties of L- and D- forms are identical; the only way they can be discriminated in the lab is by seeing which way they rotate polarized light. How could a primordial soup lead to a homochiral protocell? Unless the TM already existed to discriminate between the isoforms, the probability of getting a usable protein of any functional length is vanishingly small.,,, ,,,(it is found that) the ribosome itself participates in the rejection of D-amino acids.,,, "Collectively, these methods have allowed us to conclusively demonstrate that the ribosome itself discriminates the chirality of the amino acid",,, Natural selection could not have operated before the first accurately replicating system )i.e. ribosome) arose. But without this complex proofreading and error-correcting equipment (made up of proteins and RNA) already in operation, functional proteins would be impossible. So how did the first proteins (and nucleic acids, which are also homochiral) arise from a primordial soup of racemic ingredients? The short answer is, they didn't. The improbability of that occurring exceeds the Universal Probability Bound. An inference to intelligent causation is thus warranted. http://www.evolutionnews.org/2015/04/how_cells_keep095601.htmlbornagain77_{April 29, 2015
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Speaking of design, take a look at what the National Center For Science Education (NCSE) has to say about design ... and my own critique of that document: https://ayearningforpublius.wordpress.com/2015/03/05/what-design-looks-like-an-ncse-document-with-comments-by-don-johnson/ NCSE is predominately a bunch of Atheists using the device of censorship to keep that "divine foot" outside the door of the American public.ayearningforpublius_{April 29, 2015
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Life emerged so long ago that even the rock formations covering the planet at that time have been destroyed — and with them, most chemical and geological clues to early evolution.
This statement should be qualified with these words: "According to evolutionary theory, ...." or "We believe that ...." But they don't say that. They state this as fact! This is absolutely dishonest! It is nothing more than their opinion, their hypothesis, or rather their belief based upon their interpretation of the data.
“There’s a huge chasm between the origins of life and the last common ancestor,” said Eric Gaucher, a biologist at the Georgia Institute of Technology in Atlanta.
We would agree with the lack of evidence for abiogenesis. The data does show a huge chasm. The data cannot be argued with. But they go one step further and give us their evolutionary interpretation of the data and they give it to us as fact. Here it is: "Life emerged so long ago that even the rock formations covering the planet at that time have been destroyed — and with them, most chemical and geological clues to early evolution." In other words, we have no evidence of abiogenesis ever happening outside of the fact that life exists today. Evolutionists say the early evidence of abiogenesis is lacking because it happened so long ago that it has since been destroyed. Interesting hypothesis. How can this be tested? Certainly, that is one possible hypothesis that fits the data, but that doesn't make it true. A second hypothesis that fits the evidence just as well is that there never was any evidence of abiogenesis because it never happened. Life was created.
The stretch of time between the origins of life and the last universal common ancestor saw a series of remarkable innovations — the origins of cells, metabolism and the genetic code. But scientists know little about when they happened or the order in which they occurred.
Actually, they don't even know IF they happened. It is just assumed that all that happened by evolutionary processes because that is what the evolutionary paradigm claims.
Scientists do know that at some point in that time span, living creatures began using a genetic code, a blueprint for making complex proteins.
Welcome to the modern scientific usage of the word "know". It takes on a whole new meaning when evolutionists use the word. They do NOT know this, if you use the regular meaning of the word "know". And to pretend they do or to make such a claim creates mistrust of scientists and their claims because any educated person can see that the really do NOT know this. It is a bold yet empty claim. How could anyone possibly KNOW this in the scientific sense of the word? But does that stop them? No! They have no qualms making big bold claims like this and they ridicule the laity for not taking their word as gospel truth. Skepticism is not permitted! Little do they realize the damage they are doing to the reputation of scientists!tjguy_{April 28, 2015
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Not quite sure what your point is Dionisio @6,@7. No one doubts that things evolve. It is very interesting to understand the evolution of the design of most designed objects. Thus one can chart the evolution of bicycle design automobile design, building design, stadium design, computer chip design... All of these steps in design occurring as intelligent beings made small improvements on previous designs. All these "evolutionary" steps done by the guidance of intelligent beings optimizing for a goal. Proponents of ID certainly believe in guided evolution of designed objects. What we find impossible to believe is the unguided evolution of extremely complicated systems by random events and chance. ID proponents use of the word "evolution" is consistent. But Evolution (capital E ) proponents are inconsistent and outside the bounds of their assumptions whenever they use design language. Do you understand now?JDH_{April 28, 2015
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#6 link correction: https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/#comment-561599Dionisio_{April 28, 2015
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Article on latest OOL theory criticized for design language
They better check their own language issues (naming convention?): https://uncommondescent.com/intelligent-design/is-there-even-one-point-upon-which-there-is-universal-agreement/#comment-561601Dionisio_{April 27, 2015
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The First Gene: The Birth of Programming, Messaging and Formal Control Paperback – November 2, 2011 by David L Abel, Kirk K Durston, David K.Y. Chiu “The First Gene: The Birth of Programming, Messaging and Formal Control” is a peer-reviewed anthology of papers that focuses, for the first time, entirely on the following difficult scientific questions: *How did physics and chemistry write the first genetic instructions? *How could a prebiotic (pre-life, inanimate) environment consisting of nothing but chance and necessity have programmed logic gates, decision nodes, configurable-switch settings, and prescriptive information using a symbolic system of codons (three nucleotides per unit/block of code)? The codon table is formal, not physical. It has also been shown to be conceptually ideal. *How did primordial nature know how to write in redundancy codes that maximally protect information? *How did mere physics encode and decode linear digital instructions that are not determined by physical interactions? All known life is networked and cybernetic. “Cybernetics” is the study of various means of steering, organizing and controlling objects and events toward producing utility. The constraints of initial conditions and the physical laws themselves are blind and indifferent to functional success. Only controls, not constraints, steer events toward the goal of usefulness (e.g., becoming alive or staying alive). Life-origin science cannot advance until first answering these questions: *1-How does nonphysical programming arise out of physicality to then establish control over that physicality? *2-How did inanimate nature give rise to a formally-directed, linear, digital, symbol-based and cybernetic-rich life? *3-What are the necessary and sufficient conditions for turning physics and chemistry into formal controls, regulation, organization, engineering, and computational feats? “The First Gene” directly addresses these questions. http://www.amazon.com/First-Gene-Programming-Messaging-Control/dp/0965798895 What Utility Does Order, Pattern or Complexity Prescribe? *David L. Abel - 2011 Excerpt page 100: What scientific evidence exists of spontaneous physicodynamics ever having programmed a single purposeful configurable switch-setting? If we cannot present any such evidence, we should be self-honest enough to ask ourselves, “How long are we going to try to maintain this ruse that the cybernetic programming we repeatedly observe is only ‘apparent’ rather than real?” Has “natural process” ever been observed to write conceptual instructions? Neither reason nor empiricism has justified believing in spontaneous algorithm-writing and optimization by inanimate nature. The inanimate environment does not generate meaning, or program and optimize sophisticated formal function. Physics and chemistry do not symbolize meaning or pursue and prescribe ideal utility. Physicodynamics does not translate linear digital PI from one language into another. All of these functions are as nonphysical and as formal as mathematics itself. https://www.academia.edu/1203887/Abel_D.L._2011_What_utility_does_order_pattern_or_complexity_prescribe_In_The_First_Gene_The_Birth_of_Programming_Messaging_and_Formal_Control_Abel_D._L._Ed._LongView_Press--Academic_Biol._Res._Div._New_York_N.Y._pp_75-116 What’s the matter with evolution? Science | A ranking of the top five scientific problems found in evolutionary theory By Casey Luskin - April 25, 2015 Problem 1: No Viable Mechanism to Generate a Primordial Soup Problem 2: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code ,,, http://www.worldmag.com/2015/04/what_s_the_matter_with_evolutionbornagain77_{April 27, 2015
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"Scientists do know that at some point in that time span, living creatures began using a genetic code, a blueprint for making complex proteins..." How do they know that, exactly?arkady967_{April 27, 2015
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Coming closer to IDvolution every day.buffalo_{April 27, 2015
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As to the illegitimate use of Design language by Darwinists, it is simply impossible for them to do otherwise: In the following article, Stephen Talbott points out that it is impossible to describe the complexities of biological life without illegitimately using words that invoke agent causality:
The 'Mental Cell': Let’s Loosen Up Biological Thinking! - Stephen L. Talbott - September 9, 2014 Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”. Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness1. One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself. http://natureinstitute.org/txt/st/org/comm/ar/2014/mental_cell_23.htm
This working biologist agrees completely with Talbott:
Life, Purpose, Mind: Where the Machine Metaphor Fails - Ann Gauger - June 2011 Excerpt: I'm a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology--we simply cannot avoid them. Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn't troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it's high time we moved on. - Matthew http://www.evolutionnews.org/2011/06/life_purpose_mind_where_the_ma046991.html#comment-8858161
James Shapiro has created quite a stir in Darwinian circles by pointing out that undirected, i.e. random, causes have very little, if anything, to do with what is really happening in molecular biology:
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
bornagain77_{April 27, 2015
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OT: podcast: Birds of a Feather: Darwinian Evolution Stumped by Novel (Features) ,,,Giberson and Collins have claimed the evolution of the feather as a prime example of novel features arising by random mutation, more recent findings show how evolutionary biology is failing to provide an explanation for how this could occur. http://www.discovery.org/multimedia/audio/2015/04/birds-of-a-feather-darwinian-evolution-stumped-by-novel-features/bornagain77_{April 27, 2015
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