The origin of life

[buffalo]

rossum

I can design a simulation of clouds. Do real clouds, as opposed to simulated clouds, need a design?

I get your point. Do you get mine?

The best that can be done by scientists with respect to abiogenesis is to replicate the approximate early conditions that gave rise to life. This replication can never be exact because those original conditions for abiogenesis no longer prevail on the planet. But even a theoretical replication requires extreme aspects of design, I think you must agree.

It is not therefore possible to turn around and say, should results be fortuitous for the spontaneous appearance of life as the result of an intelligently designed experiment, that life could appear fortuitously and without design. That would not be science. That would be science fiction.

This is the position of all theists … that the entire universe, … big bang, galaxies, clouds, abiogenesis, etc. were all intelligently designed.

To say that the universe was not intelligently designed is begging the question. Where is the proof that there is no intelligent design? If humans can intelligently design their own creations, why isn’t it plausible that God could intelligently design humans? We know that if intelligent design can exist inside the universe, there is no necessary logical impediment to the existence of intelligent design* outside* the universe.

That is, there is no necessary logical impediment to the idea of an Intelligent Designer.

Is it falsifiable?

The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life

Eugene V Koonin biology-direct.com/graphics/article/email-ca.gif
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

…

The central problem: the emergence of biological evolution, the inherent paradoxes of the origin of replication and translation systems, and the limitations of the RNA world

The origin(s) of replication and translation (hereinafter OORT) is qualitatively different from other problems in evolutionary biology and might be viewed as the hardest problem in all of biology. As soon as sufficiently fast and accurate genome replication emerges, ***biological evolution ***takes off. I use this general term to include Darwinian natural selection16] along with other major evolutionary mechanisms, such as fixation of neutral mutations that provide material for subsequent adaptation 17], exaptation of “spandrels” (features that originally emerge as evolutionary by-products but are subsequently utilized for new functions) 18], and duplication of genome regions followed by mutational and functional diversification 19]. All these processes that, together, comprise biological evolution become possible and, actually, inevitable once and only once efficient replication of the genetic material is established.
The crucial question, then, is how was the minimal complexity attained that is required to achieve the threshold replication fidelity. In even the simplest modern systems, such as RNA viruses with the replication fidelity of only ~10-3, replication is catalyzed by a complex protein replicase; even disregarding accessory subunits present in most replicases, the main catalytic subunit is a protein that consists of at least 300 amino acids 20]. The replicase, of course, is produced by translation of the respective mRNA which is mediated by a tremendously complex molecular machinery. Hence the first paradox of OORT: to attain the minimal complexity required for a biological system to start on the path of biological evolution, a system of a far greater complexity, i.e., a highly evolved one, appears to be required. How such a system could evolve, is a puzzle that defeats conventional evolutionary thinking.

 

[buffalo]

The commonly considered solution is the RNA world scenario, i.e., the notion that replication evolved before translation such that the earliest stage of life’s evolution was a versatile community of replicating RNA molecules 21-23]. A central element of the RNA world is a replicase consisting of RNA. The RNA world concept is supported by the experimental discovery of diverse catalytic activities of ribozymes (catalytic RNAs) 24-27]. However, all the advances of ribozymology notwithstanding, the prospects of a *bona fide *ribozyme replicase remain dim as the ribozymes designed for that purposes are capable, at best, of the addition of ~10 nucleotides to a oligonucleotide primer, at a very slow rate and with fidelity at least an order magnitude below that required for the replication of relatively long RNA molecules 28,29]. As recently noticed by one of the leading RNA world explorers, “Despite valiant efforts,…it appears unlikely that this particular polymerase enzyme will ever be evolved to the point that it can copy RNA molecules as long as itself (~200 nucleotides)” 30]. Of course, it remains possible – and this is, indeed, the belief in the RNA world community – that other ribozymes are eventually evolved to that level; however, the evidence is lacking.
The ***second paradox of OORT ***pertains to the origin of the translation system from within the RNA world via a Darwinian evolutionary process: until the translation system produces functional proteins, there is no obvious selective advantage to the evolution of any parts of this elaborate (even in its most primitive form) molecular machine. Conceptually, this paradox is closely related to the general problem of the evolution of complex systems that was first recognized by Darwin in his famous discussion of the evolution of the eye 16]. The solution sketched by Darwin centered around the evolutionary refinement of a primitive version of the function of the complex organ; subsequently, the importance of the exaptation route for the evolution of complex systems has been realized 18]. However, origin of translation resists both lines of reasoning. Primitive translation in a protein-free system is conceivable as an intermediate stage of evolution (see below) but this does not resolve the paradox because, even for that form of translation to function, the core components must have been in place already. Speculative scenarios have been developed on the basis of the idea that even short peptides could provide selective advantage to an evolving system in the RNA world by stabilizing RNA molecules, affecting their conformations or enhancing their catalytic activities 31-33] (see Ref. 34] for an attempt of a synthesis on this direction in the study of translation origins). These ideas are compatible with observed effects of peptides on ribozyme activity 35] but none of the scenarios is complete or supported by any specific evidence, and all include reactions without precedent in modern biological or model systems.
**All this is not to suggest that OORT is a problem of “irreducible complexity” and that the systems of replication and translation could not emerge by means of biological evolution. It remains possible that a compelling evolutionary scenario is eventually developed and, perhaps, validated experimentally. However, it is clear that OORT is not just the hardest problem in all of evolutionary biology but one that is qualitatively distinct from the rest. **For all other problems, the basis of biological evolution, genome replication, is in place but, in the case of OORT, the emergence of this mechanism itself is the explanandum. Thus, it is of interest to consider radically different scenarios for OORT.

buffalo’s commentary - nope - not to suggest irreducible complexity. We will just postulate really huge odds. And of course the Multiverse world suggests that all possible worlds exist, even fake ones and maybe this one with a God.

 

[rvilbig]

You cannot just assume what you want to prove. I agree that you cannot originate a simulation without a design. However, we are not discussing the origin of simulated life, we are discussing the origin of life.

I can design a simulation of clouds. Do real clouds, as opposed to simulated clouds, need a design?

rossum

Cloud patterns have to do with the kinetic theory of gases, which are statistical distributions. These involve laws (the distribution itself) and chance (that this particular molecule has this particular property.) We can all agree that the law is indicative of order and hence an Orderer.

However, I think most atheists point to the “chance” part and claim it must be random, and thereby make randomness their god. Christians have a Scriptural answer to this, to quote Saint Paul: “What therefore you unknowingly worship, I proclaim to you.The God who made the world and all that is in it, the Lord of heaven and earth.”

Within the Catholic faith, there is indeed a tradition of recognizing that God is the cause of all chance outcomes, and we owe Him thanks and praise when this results in our good fortune. Consider the name Saint Francis of Assisi gave to Giovanni di Fidanza when he was cured of a childhood illness: Bonaventure, which is Latin for “good fortune.” Anyone who has read the writings of the Seraphic Doctor knows what good fortune this chance outcome was for later generations. Perhaps we ought to follow St. Francis’s example and exclaim “Bona ventura” when we see the good fortune that is ours from the “chance” processes of evolution.

Hope this helps,

-Ryan Vilbig
ryan.vilbig@gmail.com

 

[Charlemagne_II]

Perhaps we ought to follow St. Francis’s example and exclaim “Bona ventura” when we see the good fortune that is ours from the “chance” processes of evolution.

Chance has nothing to do with it. Do you mean we might not have come to exist? Then why would the Creator bother to create? The universe was designed to produce man.

“For thus says the LORD, The creator of the heavens, who is God, The designer and maker of the earth who established it, Not creating it to be a waste, but designing it to be lived in: I am the LORD, and there is no other.” Isaiah 45:18

 

[Charlemagne_II]

buffalo

Is it falsifiable?

Is abiogenesis by chance falsifiable?

 

[rvilbig]

Perhaps we ought to follow St. Francis’s example and exclaim “Bona ventura” when we see the good fortune that is ours from the “chance” processes of evolution.

Chance has nothing to do with it. Do you mean we might not have come to exist? Then why would the Creator bother to create? The universe was designed to produce man.

“For thus says the LORD, The creator of the heavens, who is God, The designer and maker of the earth who established it, Not creating it to be a waste, but designing it to be lived in: I am the LORD, and there is no other.” Isaiah 45:18

Perhaps that the world is not a waste is due to the law part of the kinetic gas theory and QM, etc, as I wrote in my post. However, it is indeed true that we are contingent beings and that we may have been otherwise or not at all. Of this we read in the Psalms: “When you take away their breath, they perish and return to the dust from which they came. When you send forth your breath, they are created, and you renew the face of the earth” (Psalm 104:29-30). Indeed, the LORD, the creator of the heavens, is the God of our Bonaventure: our good fortune.

-Ryan Vilbig
ryan.vilbig@gmail.com

 

[redneck22]

Venter’s claim on “Creation”

Interesting link, here is an extract of Elizabeth Pennisi’s summation of the results from sciencemag.org/cgi/content/full/328/5981/958

"It was achieved at great expense, an estimated $40 million…

The researchers started building their synthetic chromosome by going DNA shopping. They **bought **from a company more than 1000 1080-base sequences that covered the whole M. mycoides genome; to facilitate their assembly in the correct order, the ends of each sequence had 80 bases that overlapped with its neighbors." (emphasis mine)

The look on naturalists faces when you tell them it cannot assemble itself “naturally” is PRICELESS…for everthything else there’s Mastercard.

 

[rossum]

The species cloud does not occur on it’s own. It is designed by the process that creates it; it does not emerge out of nothing with no cause.

You could argue that it does not require a conscious designer, but it must be designed nonetheless.

Cause does not equate to design. Clouds do indeed have a cause, but they do not have design.

rossum

 

[rossum]

Patterns can occur naturally. Designs are based on language and symbols. DNA is a language. Designs always contain patterns but natural patterns do not contain symbols or language. The earliest life exhibits hallmarks of design.

DNA is not a language. It is a series of chemical linkages, all of which are explainable in terms of chemistry. I will agree that sometimes we use ‘language’ as an analogy to describe DNA but you are pushing the analogy too far if you take that as the real nature of DNA. DNA is a chemical, not a language. We can but jars of powdered DNA; can we buy jars of powdered language?

rossum

 

[rossum]

Since simulations are used in science, is there any criteria for simulations?

Accuracy. The figures we get out of the simulations are checked back against the data from the real world. If the match is close enough then we know that the simulation is good to that degree of accuracy.

What kind of data would be needed to create the simulation of something real? Suppose no one really knew the real thing, e.g., how life originated, including human life, how could a simulartion be created?

We start with different hypotheses as to how it happened. Each hypothesis lets us try some simulations/experiments. Where we get bad results we drop those hypotheses. Where we get good results we extend those hypotheses.

For example the Miller-Urey experiment confirmed one hypothesis about the origin of amino acids on the early Earth.

rossum

 

[Bob_Crowley]

Water is inanimate. Drink some water. That water you drink is incorporated into your living body so it becomes animate matter. Take some iron tablets. The iron in those tablets is inanimate. That iron becomes incorporated into your body so it is now animate.

There is nothing special about the chemicals in a living organism. They are just chemicals.

rossum

The chemicals are just chemicals. But there has to be a pre-existing biological machine there for them to do their work within the machine.

 

[rossum]

The best that can be done by scientists with respect to abiogenesis is to replicate the approximate early conditions that gave rise to life. This replication can never be exact because those original conditions for abiogenesis no longer prevail on the planet.

Welcome to science. Science does not give exact answers, it gives approximate answers to a known level of approximation. Yes, our simulations will never be exact. For one thing our labs are always going to be smaller than the original early Earth.

But even a theoretical replication requires extreme aspects of design, I think you must agree.

Of course. It is designed to replicate a previous event. That does not make the original event designed. If I make a laboratory scale replica of God does that mean that God Himself must have been designed by some higher entity?

This is the position of all theists … that the entire universe, … big bang, galaxies, clouds, abiogenesis, etc. were all intelligently designed.

Agreed. The problem here is one of definition. All theists agree with what you say. However, what the Discovery Institute calls ID is something different:* Theistic ID: the entire universe and all living things were designed by God.

• DI-ID: we can scientifically detect design in modern living organisms.

The first position (T-ID) is compatible with all of science. Like theistic evolution is takes the position that science is elucidating the methods that God used for his purpose. DI-ID is different as it is in opposition to science, asserting that science is incapable of elucidating all of God’s methods and required some miraculous tinkering with DNA or whatever along the way.

If humans can intelligently design their own creations, why isn’t it plausible that God could intelligently design humans?

God is a theological entity, not a scientific entity. If there is some scientific evidence for God then we can talk again. Currently there is precisely as much scientific evidence for God as there is for Allah, Zeus, Vishnu, Durga and all the others. Science treats all of them in the same way. Individual scientists are free to believe in any or none of them.

That is, there is no necessary logical impediment to the idea of an Intelligent Designer.

I agree. An Intelligent Designer can be taught in logic class. The concept has no place in science class unless and until there is scientific evidence of the existence of the designer or designers. Science has no problem with design, as in archaeology or forensic science, where the existence and capabilities of the designers are known. Science does have problem with “life on earth was caused by aliens from planet Zog” when there is no evidence to show the existence of any life at all on planet Zog.

rossum

 

[Thing]

Accuracy. The figures we get out of the simulations are checked back against the data from the real world. If the match is close enough then we know that the simulation is good to that degree of accuracy.

We start with different hypotheses as to how it happened. Each hypothesis lets us try some simulations/experiments. Where we get bad results we drop those hypotheses. Where we get good results we extend those hypotheses.

For example the Miller-Urey experiment confirmed one hypothesis about the origin of amino acids on the early Earth.

rossum

Simulations. Thats an interesting idea. So I put carbon, oxygen, hydrogen, iron, calcium etc., atoms into a bucket of water at 20 degrees C for how long - 200,000,000 years and I will get new life created - bacteria perhaps. Is this happening today anywhere?

 

[rossum]

Is it falsifiable?

Evolution has been falsifiable since 1859; Darwin described how to do it and Behe’s IC was an attempt to follow one of Darwin’s proposed falsifications. ID has yet to answer the question as to how it could be falsified.

We can easily describe something that cannot evolve. ID has yet to describe something that their proposed designer could not design.

Perhaps you can answer my question Buffalo: Is there anything that we might possibly discover that the proposed Intelligent Designer could not have designed.

How can we falsify ID?

rossum

 

[rossum]

Simulations. Thats an interesting idea. So I put carbon, oxygen, hydrogen, iron, calcium etc., atoms into a bucket of water at 20 degrees C for how long - 200,000,000 years and I will get new life created - bacteria perhaps. Is this happening today anywhere?

The bucket needs to be the size of a planet, and you will need the energy (name removed by moderator)ut from a nearby star which needs to be in your laboratory as well. May I suggest that you apply to Magrathea, when they reopen for business, to build your lab for you.

New life arising today is unlikely since we now have an oxygenating atmosphere, whereas Earth used to have a reducing atmosphere, and a reducing atmosphere seems to be required by the chemistry. Even if something did manage to get started it would quickly get eaten by bacteria. Think of a hungry adult tiger fighting a new-born baby.

rossum

 

[Thing]

The bucket needs to be the size of a planet, and you will need the energy (name removed by moderator)ut from a nearby star which needs to be in your laboratory as well. May I suggest that you apply to Magrathea, when they reopen for business, to build your lab for you.

New life arising today is unlikely since we now have an oxygenating atmosphere, whereas Earth used to have a reducing atmosphere, and a reducing atmosphere seems to be required by the chemistry. Even if something did manage to get started it would quickly get eaten by bacteria. Think of a hungry adult tiger fighting a new-born baby.

rossum

I liked Slartibartfast, the coastal designer.

 

[rvilbig]

I agree. An Intelligent Designer can be taught in logic class. The concept has no place in science class unless and until there is scientific evidence of the existence of the designer or designers. Science has no problem with design, as in archaeology or forensic science, where the existence and capabilities of the designers are known. Science does have problem with “life on earth was caused by aliens from planet Zog” when there is no evidence to show the existence of any life at all on planet Zog.

rossum

While I absolutely prefer the word “evolution” to “intelligent design,” as do Fr. George Coyne, director of the Vatican Observatory, and the last two popes (JPII, BXVI), I still think we must realize that evolution proceeds along an intelligent course. Furthermore, this discussion is relevant to findings in nature and the construction of phylogenetic trees.

Consider the platypus: a mammal with a bill, webbed feet, and a venom gland. It also lays eggs. Since the evolutionary line that includes mammals diverged long before the appearance of birds and reptiles, these features emerged in evolution twice. What does this reveal about evolution, you might ask? Newman offers an interesting answer:

“It is prima facie unaccountable that an accident should happen twice… If we expect a thing to happen twice, it is because we think it is not an accident, but has a cause. What has brought about a thing once, may bring it about twice. What is to hinder its happening? rather, What is to make it happen ? Here we are thrown back from the question of Order to that of Causation. A law is not a cause, but a fact; but when we come to the question of cause, then, as I have said, we have no experience of any cause but Will. If, then, I must answer the question, What is to alter the order of nature ? I reply, That which willed it;” (Grammar of Assent, p 71-72).

Hope this helps,

-Ryan Vilbig
ryan.vilbig@gmail.com

 

[buffalo]

DNA is not a language. It is a series of chemical linkages, all of which are explainable in terms of chemistry. I will agree that sometimes we use ‘language’ as an analogy to describe DNA but you are pushing the analogy too far if you take that as the real nature of DNA. DNA is a chemical, not a language. We can but jars of powdered DNA; can we buy jars of powdered language?

rossum

We are not talking DNA the molecule. We are talking the DNA code.

The DNA code has all the characteristics of a language. Linguistics are being used today to study it. You can still hold-out but time will catch up with you rossum. You will eventually have to agree that the DNA language comes from a mind.

 

[buffalo]

Evolution has been falsifiable since 1859; Darwin described how to do it and Behe’s IC was an attempt to follow one of Darwin’s proposed falsifications. ID has yet to answer the question as to how it could be falsified.

We can easily describe something that cannot evolve. ID has yet to describe something that their proposed designer could not design.

Perhaps you can answer my question Buffalo: Is there anything that we might possibly discover that the proposed Intelligent Designer could not have designed.

How can we falsify ID?

rossum

Himself.

failed predictions.

 

[grannymh]

Original question.

Originally Posted by grannymh forums.catholic-questions.org/images/buttons_khaki/viewpost.gif
Since simulations are used in science, is there any criteria for simulations?

Answer.

Accuracy. The figures we get out of the simulations are checked back against the data from the real world. If the match is close enough then we know that the simulation is good to that degree of accuracy.

Checking back to the real world only works for recent centuries when various people recorded various observations or preserved ancient Greek and Chinese writings.

For example, an assumption is made that the data for mathematical formulas recorded during the Renaissance is accurate or that it generally represents the real world of that period. We can compare early mathematical formulas with current ones based on our own observations and study.

On the other hand, when considering the origin of life, specifically human life, what data is there from the real world during that time period? Currently, simulated population estimates can be based on average time lengths for a generation. There is a question concerning how to factor in overlapping generations – if overlapping generations were a normal and regular occurrence? Note: I am aware that researches have already proposed various solutions to that question. However, again we are dealing with assumptions based on current studies which may or may not reflect the actual activity in the real world millions of years ago.

I do not understand how simulations can work for millions of years ago when studies in geology and environmental science demonstrate millions of major and minor changes which have occurred since earth formed.

In my own back yard, I’ve watched grass cover cement and form a base of roots and dirt which unchecked would eventually obliterate the cement from sight. What kind of information have volcanoes obliterated from sight? The point is that data which accurately describes conditions during millions of years backwards in time is actually an unverifiable assumption.

Blessings,
granny

Human nature is unique in all the universe.