Definition of life: Amino acids, sugars could be “very primitive and simplistic life forms”?

_{Denyse O'Leary

February 16, 2012

News, Origin Of Life}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

Readers may recall Edward Trifonov’s new, brief definition of life (after studying 123 previous ones):

Life is self-reproduction with variations.

He offers some further thoughts in “What Is Life?” (The Scientist, February 16, 2012):

The border between life and nonlife may, actually, be placed anywhere within the realm of the abiotic processes. Oligonucleotides, oligopeptides, nucleobases, amino acids, sugars—all could be considered as very primitive and simplistic life forms, if the definition is extended (and simplified) to the very elements. Before 1828, when organic substances could be found only within living matter, the popular idea of a “vital force” reigned. In those days, one could draw the life/nonlife border at the first appearance of the small “vital force” (i.e., organic) molecules. Abiotic synthesis of urea by Friedrich Wöhler in 1828 dethroned this common belief.

The hypothetical primitive RNA replication process has a degree of sophistication that separates it from mere chemistry: it copies itself and allows copying mistakes, which themselves are copied in future generations. In other words, this is the process of self-reproduction with variations (as in Spiegelman’s system), not just organic synthesis.

Trifonov lost some of us at “hypothetical primitive RNA replication process.” If it’s hypothetical, it is neither life nor not-life; it is an abstract idea that may or may not have a counterpart in nature

.In any event, thoughts?

Comments

Hi Eric @7- did that sterile animal come from reproduction? As far as I know mules- sterile animals- come from the mating of a horse and a donkey, ie from reproduction. That is why I put that in there-> to account for sterile organisms. So if you can't reproduce you will still satisfy the "came from reproduction" part.Joe_{February 18, 2012
February
02
Feb
18
18
2012
07:47 AM
7
07
47
AM
PDT}

Joe @6: Does this mean that an animal that is born sterile is not alive? Jus' sayin' . . .Eric Anderson_{February 17, 2012
February
02
Feb
17
17
2012
08:27 PM
8
08
27
PM
PDT}

felipe- You need to be able to reproduce or have come from reproduction.Joe_{February 17, 2012
February
02
Feb
17
17
2012
04:18 AM
4
04
18
AM
PDT}

Invivoveritas, "One barrier might be that we assume a pure materialist posture when investigating life." This is the most startling feature of the scientific establishment's current paradigm. What new discoveries have induced ANY of the best of its physicists, to renounce the utterly certain belief in ID, shared by the most (succesfully) innovative scientific thinkers of the 20th and 19th centuries?) The application of the remark of IDer, Wolfgang Pauli, after reading a student's paper that it was 'not even wrong', might, pre-eminently, have been coined to describe materialism with its belief in random design: designs that were not designed, but are propitiously accidental. Assuming the inconceivable, that the universe came together and is sustained by an endless series of accidents, why should those accidents always be so propitious that, in their beauty, alone, some of the products of this eternal seredipity, should be so magical as to stir our souls; great music, great works of art, feelings of compassion, religious devotion, etc. 'It's not even wrong', because it doesn't even reach a level of reason that is intelligible on even the most rudimentary level. Science, essentially, has nothing to do with the question. Not because empirical science is, by the limititions of its nature, such a base discipline, although that is the case, or that the philosophy of ID is super-sophisticated. It is, on the contrary, simply that any adult foray into the world of reason is super-sophisticated in comparison with it. It quite literally 'isn't even wrong', because it has no experiential point of comparison, no identifiable framework of reference at all; it is gratuitous, it is arbitrary, it is irrational. This is the reason why arguing with materialists on here is irredeemably tedious. They are so horrendously inapt for conceptual thinking that they think it's about the biology, etc., when the there is nothing in our experience of this world that can render it intelligible.Axel_{February 17, 2012
February
02
Feb
17
17
2012
03:22 AM
3
03
22
AM
PDT}

Here are some random thoughts related to the “Definition of Life” topic. • Like everybody else I tried to identify all relevant characteristics of life, but this plan did not last much. • However I found interesting that, besides the characteristics of life enumerated by others (can reproduce, features high degree of autonomy, homeostasis, etc.) I think we should enumerate other important characteristics of life that should not be absent from any attempt to define it. o Life is wonderful. Unless you are miserable after a personal failure or disappointment. o Life is miraculous – maybe because we have difficulty to define it. • Let’s do a little bit of analysis. Let’s take the electron. What would be the definition of an electron? We know the stories. First, we and scientists at the beginning of the 20th century “defined” the electron as a minuscule material ball with a negative electric charge that rotates around another minuscule material ball - the nucleus – like a planet around its star. Smarter scientists, decades later told us that this definition of the electron is mistaken. The real definition involves a picture in which there is an “electron cloud” where an electron loses its citizenship as a corpuscular ball and becomes more of a hard to grasp abstraction: an “electron cloud”. In this electron cloud you can know the electron position at a time T – but you cannot know its speed at the same time T. Or you can measure its speed at time T – but in that case you are condemned to have no clue where it actually is at time T. The short story for me is that the smartest and most advanced particle physicist cannot give a satisfying DEFINITION of an electron, and I guess the common sense conclusion is to recognize that the word “electron” becomes more of a “name” designating a controversial being with a dubious personality and ghostly existence. Consider another thought that continues to torture me – as I found out torture: how come the world that at the atomic level is so airy, with minuscule particles (electrons) circling at vast distances around other minuscule ones (atoms) or otherwise making a fluffy cloud around them – at the macro level appears to all of us to be hard, almost impenetrable matter – at least for solid staff? • What can I learn from this particular analysis? Maybe no one can give a satisfying definition of an electron, and maybe of many other “things” in nature. • On this way of thinking, trying a definition of life seems orders of magnitude more challenging than the definition of the electron – although I recognize that the two are logically part of different “categories” • Next step: try to move from analysis to synthesis. • Maybe we can classify our human knowledge in some interesting categories. • A lot of our knowledge can be categorized as OBSERVATIONAL knowledge. For example, the laws of physics like laws of electromagnetism, gravitational law, laws of chemistry, relativity, etc. it seems to me falls under this category: scientists observed natural phenomena, measured, speeds, forces, accelerations, and captured some observed invariants into mathematical equations and formulas, or chemical reaction rules. What is interesting is that there is no actual guarantee that these laws (observational knowledge) are absolutely true. The moment an exception can be observed/demonstrated, the law may need to be re-evaluated or corrected. This is illustrated by the parable with the rule that “all craws are black”, that can be upset as soon as someone will come out and show scientific community a white feathered craw. • So, our most advanced (in some sense) knowledge is of OBSERVATIONAL type. • I would think of a different type of knowledge which might be distinct from the OBSERVATIONAL knowledge, but I am not absolutely sure about this. Maybe some overlapping exists between the two. I would call this category as OPERATIONAL knowledge. For example, if I am a carpenter, I know how to build the wood frame of a house. If I am a software engineer I know how to write programs that most of the time work as expected. The OPERATIONAL knowledge is captured in books, training materials, professor minds or in the professional minds or in the mind and the hands of a lady who knows how to knit a fine wool sweater. • Coming back to the initial proposal of finding the DEFINITION OF LIFE, I can say the following. A molecular biologist a geneticist, a blogger, a software engineer can have an OBSERVATIONAL knowledge of life at various levels of depth and breadth. Again, a surgeon, a nurse, a mother, a chef have very valuable OPEERATIONAL knowledge about life. But none of these and none of us have what I would call a FOUNDATIONAL knowledge of life. • Now this is the third kind of knowledge: FOUNDATIONAL knowledge. I would say someone who knows what is the ULTIMATE ESSENCE of an electron has FOUNDATIONAL knowledge about the electron. This foundational knowledge implies that that someone will know what it is (even if it’s only an abstraction, a thought or whatever is its ultimate essence) and this knowledge is sufficient to create from scratch an electron from primary essences and knows how to make it dance or behave as a good citizen or otherwise. We can talk about FOUNDATIONAL knowledge for other “tough” subjects for philosophers, scientists and all of us. For example, what is the foundational knowledge about TIME, about SPACE, about LIGHT. And sure the foundational knowledge about life. • It appears to me that we humans possess in various degrees OBSERVATIONAL knowledge and OPERATIONAL knowledge and we thirst after FOUNDATIONAL knowledge. • My intuition is that FOUNDATIONAL knowledge is beyond our touch. In other words, the FOUNDATIONAL knowledge is super- natural. Someone who claims FOUNDATIONAL knowledge about a thing should be able to demonstrate that can create that thing from scratch, because he possesses the knowledge of its essences and knows how to put them together into that thing by himself with no help or starting pre-conditions. • There is plenty of OBSERVATIONAL and OPERATIONAL knowledge about life that we can still acquire. It seems that there are layers and layers of knowledge in the living word, in the life at the microbiological level, cellular level, all systems levels to be acquired, understood, organized, and harmonized. There may still be significant barriers to observe and acquire this knowledge because of difficulties to investigate it at the molecular level and “in vivo”, to understand the information stored and processed in the cells, tissues, organs, bodies, brains. One barrier might be that we assume a pure materialist posture when investigating life. • I wonder also if it’s possible that we can give REAL definitions ONLY FOR ABSTRACTIONS. For example, we can have, unchallenged definitions for what is a triangle, what is an isosceles triangle. We can talk also about the definition of a table, but in this case we really think of the definition of an abstraction of a table: we have a mental concept of what is table: a material flat platform supported by one or more material legs. If we talk about the definition of an electron, the definition of a planet, of a star, of a galaxy, of the Universe, we can build a definition of an abstraction of that entity with a higher or lower level of detail or accuracy, but we have no clue how that real type of entity is constructed (can be constructed) from ground up, which would show that we are intimate with all its parts, its articulations of the parts and internal workings. Sure, we can create hypotheses about how that entity formed, or can be formed, but so far it is beyond our power to demonstrate or verify that our hypotheses come any close to reality. • Thinking about the isosceles triangles, I started having seconds thoughts about FUNDAMENTAL knowledge related to abstractions. Is it possible that we may acquire fundamental knowledge about plane triangle geometry? I have an inclination to say that if you know a lot of Euclidian geometry you know a lot of axioms, theorems and properties of triangles in plane geometry and all their elements, you may possess foundational knowledge about triangle geometry. But again, thinking that you may never know ALL possible theorems and properties of triangle geometry the answer is that even for (relatively simple) pure abstractions we cannot have fundamental knowledge.InVivoVeritas_{February 17, 2012
February
02
Feb
17
17
2012
01:50 AM
1
01
50
AM
PDT}

Replication seems to be quiete a poor definition of Life Might be for unicellular organisms But what about ME ? Do I replicate myself? If I have no offsprings am I still a living beeing? May be my cells ar alive but not me...felipe_{February 16, 2012
February
02
Feb
16
16
2012
11:18 PM
11
11
18
PM
PDT}

I'm not clear on the "variations" part. Why are variations needed for something to be alive? This seems like a hold-over concept from the traditional evolutionary idea of how life progresses to new forms -- random variations + selection. But surely whether something reproduces with variations or reproduces without variations isn't germane to whether it is alive. So we are left with just self-reproduction? Incidentally, something like the "vital force" separating life from non-life exists. Today we call it complex specified information.Eric Anderson_{February 16, 2012
February
02
Feb
16
16
2012
11:11 PM
11
11
11
PM
PDT}

a note as to how far removed his 'hypothetical primitive RNA replication process' is from reality;
Origin of Life: Claiming Something for Almost Nothing - March 2010 Excerpt: Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.” But does this work support a naturalistic origin of life? A key question is whether the molecule would form under plausible prebiotic conditions. Here’s how the paper described their work in the lab to get this molecule: RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring. Solid was then redissolved in 2 mL pyridine. Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution. Solution was stirred at room temperature for 4 h. All solutions were sequestered from exposure to air throughout. Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation. Remaining solvent evaporated overnight in a vacuum chamber. Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution). Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated. Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU. PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6. Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%. Even more purification and isolation steps under controlled conditions, using multiple solvents at various temperatures, were needed to prevent cross-reactions.,,, (here is a understatement of the year) It is doubtful such complex lab procedures have analogues in nature. ,,,, http://www.creationsafaris.com/crev201003.htm#20100302a
(intelligence is clearly required for even this meager step),,, the problem of sequencing the nucleotides – the key question – has not been addressed. Where did the genetic code come from? One ribozyme is not a code!!!,,, any scientists who believes this comes anywhere near answering the 'information dilemma' should immediately step away from the chemical fumes in the laboratory!!!bornagain77_{February 16, 2012
February
02
Feb
16
16
2012
06:26 PM
6
06
26
PM
PDT}

You must be logged in to post a comment.

Leave a Reply