Evolution : a process of ‘change’ not of ‘start’

Discussions on general biology and biological evolution, genetics, zoology, ecology, botany, etc.

Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 2nd, 2020, 6:38 am 

Forest / davidm

I agree with Forest_Dump — our being here is basically chance, though not entirely so — natural selection is not chance, though it is unpredictable, and clearly follows no pre-determined pathways. However, the feeders of natural selection — mutations — are chance, uncorrelated to the environment. Humans were not inevitable, for example.


The trouble with saying that it all boils down to chance is that when you are confronted with the odds, you argue rightly that it cannot be down to chance, but to process. So when Dawkins and others do say - 'what process?', and 'what could provide a drift towards DNA and replication?', we are back onto the difficulties that prior to the first cell there is no known replication process on the active chemicals required for life.

It may well be that some will emerge later, but as things stand, there is only potential and hope.

The transition point(s) between our definitions of chemicals vs life is not just an academic topic that might tick off the religious interest; it/they could unlock our entire understanding of physical life as we know it. I feel it is worth debating.

When DNA is a code - what could truly lead to the development of a code?
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 2nd, 2020, 6:53 am 

Hi Hyksos

My examples were more relevant than Homologous Recombination. Your central dogma in this thread is that unthinking chemical processes could never give rise to conceptual purposes.

But bacteria read DNA. They do so effectively and correctly. I have personally worked with restriction endonucleases under lab conditions. I can report to you that they identify a particular sequence of base pairs and bind to it having found it. It is not a matter of near-misses. Rendos identify a subsequence with the precision that I can only describe as the precision of a laser. It's like watching a computer text-search a single word appearing in a large novel and finding it, every time.


I feel that the issues are not the same as Homologous Recombination, because the processes you describe do not seem to indicate anything other than a mechanical action of chemical change. Such changes and the compatibility issues they bring, (by introducing new and untested combinations of DNA) do not produce a conceptual challenge because the new entity will survive or fail on the vagaries of circumstance.

Homologous Recombination is not producing change but effecting a variable process with a outcome that we can anticipate - not some arbitrary concoction. The processes observed do not rely on an enzyme (or such other chemical) where its shape and chemical composition mean that it will only work in certain places. The processes of Homologous Recombination seem to analyse and compare sequences of DNA in order to reconstruct sections of DNA that have been entirely destroyed - a conceptual purpose perhaps - but how else can you describe it?

I do not see that in bacterial or viral change.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 2nd, 2020, 7:08 am 

davidm

You invoked an author. I quoted his own words, and yours, in responding. You have pretty much ignored my responses, preferring to complain instead — as you are doing again in this post.


You suggested that the author was some sort of lunatic and pointed to articles in Wikipedia that actually verified everything the author had said. What sort of comment is that?

The point about supposed evolution prior to the first cell is that there is no evidence for a mechanism that could allow it to evolve. It is purely wishful thinking on your part, and when you are confronted by the challenges which this poses, you blindly revert to saying that it is therefore just a matter of chance... until you are confronted by the odds and you then reverse again.

Something has to break this deadlock in your thinking and I would like to explore scientific ideas that would help resolve the issue. As far as I can see, you have merely wanted to sling mud.

I said...
I totally agree that chemical change doesn't have a sense of direction, but people like Dawkins in their books such as the Blind Watchmaker, and the God Delusion absolutely talk about a sense of direction achieved through better survival and the desirability of attributes when selecting a mate etc.

You then said
You misinterpret Dawkins — as I believe I have explained to you. Did you notice the word “blind” in Blind Watchmaker? It is a metaphor by Dawkins. It means evolution is blind — no foresight, no planning, goal or direction, and certainly no control. You mention the desirability of attributes when selecting a mate. This is called sexual selection, and is certainly a driver of evolution.


I have answered this point and Dawkins own books are evidence that he does use such mechanisms as a way to accelerate the development of a species.

Perhaps you would like to comment on the topic of this debate - what were the equivalent influences (prior to the life/the living cell) that would allow the development of the DNA code?
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 2nd, 2020, 12:43 pm 

The trouble with saying that it all boils down to chance is that when you are confronted with the odds, you argue rightly that it cannot be down to chance, but to process.


Who is “you” here? I argue that the start of life can come down to chance — and apart from natural selection, the process of evolution is a chance process.

Yes, evolution itself is a “process,” but a process does not have to imply direction, intent, goal or telos. And evolution manifestly does not exhibit these traits — just the opposite.

Moreover, you have no way to calculate the odds of life starting by chance — whether the odds were good or bad. So appeals to the “odds” are empty. Even if the odds of life starting by chance were poor (and we don’t know this), highly unlikely occurrences happen all the time. If it can be calculated that some event occurs only once in a billion trials, then the chance of it occurring, after one billion trials, converges to unity — 1:1. The earth, and the universe, are full of chancy, undirected chemical encounters — such trials far exceed billions of trials. Evidence suggests that the universe is spatially infinite, and isotropic and homogenous everywhere. In such a universe, an infinite number of chancy trials will be carried out. In that case, then life, no matter how unlikely to arise — and we don’t know that it is likely, or unlikely — will arise on an infinite number of worlds. We know thus because it arose at least once — here. With an infinite number of trials, any event with a nonzero chance of occurring, can be expected to occur an infinite number of times.

Moreover, you seem to setting up a false dichotomy between chance and “control,” whatever you mean by that. The actual opposite of “chance” (strictly, contingency) is (logical) necessity. In the real world, lots of things are partly chancy — partly contingent. Mutations occur by chance — are random with respect to fitness. But then natural selection, without control or intent or mind, mediates chance mutations to produce changes in populations. Drift — entirely chance — also produces changing populations. These (non-controlling) processes are actually entailed by reproduction with variation in ever-changing environments.

Two strangers may meet, by pure chance, on a street corner, and fall in love on sight, because they have certain affinities for each other. The meeting was pure chance, but the affinities were inbuilt, waiting for a chance encounter to activate them.

Same thing with nature. Certain atoms have certain (well understood) affinities for each other, though they will come together by chance. Chance encounters of hydrogen and oxygen yield water. By chance alone, three spatial dimensions pop out of the big bang. But in a 3D world, gravity and other processes are necessarily described by the inverse square. In a universe of four spatial dimensions, the inverse cube would necessarily obtain.

The start of life was surely like that. There were tons of variegated, chancy chemical processes going on, over vast periods of time. Some chemical bonds, affinities, happened by chance over time, and led to simple replicators that became subject to selection. No “control” needed, or present.

So when Dawkins and others do say - 'what process?', and 'what could provide a drift towards DNA and replication?', we are back onto the difficulties that prior to the first cell there is no known replication process on the active chemicals required for life.


You shouldn’t fool yourself into thinking that Dawkins would agree with anything you have said in this thread. You continue to misrepresent him.

More, you seem, here, to be saying that in order to produce replicators, prior replicators are needed. This is not so. Simple replicators arose from non-replicators. We can actually observe this in nature without reference to life. Someone strikes a match (non-replicator) to dead leaves in a dead forest (also non-replicating). The fire quickly spreads — it replicates. Hence we have a straightforward account of a replicative process arising from non-replicating antecedents.

When DNA is a code - what could truly lead to the development of a code?


Evolution.

Now if you are asking what made the first rudimentary replicators that eventually evolved the DNA “code,” then you are just asking how abiogenesis occurred. We don’t know. BUT, there are tons of plausible and theoretically testable hypotheses — I gave you a whole Wiki page of them. Did you read them?

This is why, here, you are regurgitating a standard-issue “gap” argument, or an argument to incredulity: We don’t know how x occurred, and you are incredulous that it could have occurred by chance alone, or by some combination of chance and physical regularities: therefore, you put God, ID, “control” or something else into that gap. This is not science or even philosophy. It is empty.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Serpent on February 2nd, 2020, 3:03 pm 

What was the chance of life arising on this planet?
100%
EtC: 99.7% There is a possibility that it was imported from elsewhere.
What is the chance of life arising on any other planet?
We have no way to calculate. There is insufficient data regarding both the planets and the possible ways and circumstances in which life can arise.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby hyksos on February 3rd, 2020, 12:14 am 

Serpent » February 2nd, 2020, 6:04 am wrote:The thread title gives the gist of lateralsuz's argument (as I imperfectly understand it), which might be stated as
"Evolution is acceptable as an explanation of everything that happens after the first reproductive cell.
But it doesn't explain how the first cell got to be alive."
I'm comfortable with my inability to explain that.

It would be disingenuous of all of us to claim this question is not well-grounded. (It is.)

It would doubly disingenuous to claim that science has lain the question to rest. (It hasn't)

Books worth of ink have been spilt on this topic. Our best educated hypothesis is that it has something to do with the relationship between open thermodynamic systems and order creation. Chemical soups with energy going into them are known to enter cycles called autocatalysis.

It is still (provably) true that dead, inorganic, matter would never form into a living entity. That is, I believe, prohibited by the 2nd Law. But open thermodynamic systems are being fed usable energy at the expense of their surroundings. The 2nd Law does not apply, and there is generally no telling what may happen to its dynamics.

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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 3rd, 2020, 11:32 pm 

davidm

Yes, evolution itself is a “process,” but a process does not have to imply direction, intent, goal or telos. And evolution manifestly does not exhibit these traits — just the opposite.


In terms of the evolutionary process as normally described, I agree.

Moreover, you have no way to calculate the odds of life starting by chance — whether the odds were good or bad. So appeals to the “odds” are empty.


I am sorry but that is verging on rubbish. The odds of a single protein emerging by chance are easily calculated, (and have been done so in many books - such as The Origins of Existence by Fred Adams - and I believe Dawkins too). It is a product of the number of types of amino acid components used, the length of the protein chain; and the exact precision of the sequence needed. In short, the authors that I have read, all agree that there are more combinations of amino acid components in one average length protein than there are atoms in the universe. Hence the odds - especially when different randomly emerging proteins have to somehow find each other and work in harmony with each other - presumably by chance as well.

The 'off the scale' odds are very real without a prior process to help them.

In the Blind Watchmaker, Dawkins takes this even further by applying a generous (quick) rate of change to the equation, to say that there isn't logically enough time to generate the first cell in the earth timescales we know of, by simple chance.

It is therefore necessary to have a process which will shorten the timeframes - and as part of this, it is necessary to have a reliable means of exact replication. This is because the process needs to experiment on, and adapt, things that have already emerged so as to avoid re-inventing the original protein from scratch each time. If you wait a billion years for a protein and then screw it up on your first experiment, then you need a reliable source of others so that you don't have to wait another billion years for the next one.

However the odds are so large that even if a single useful protein did emerge in a modest timescale - they next one would probably never emerge after that by chance alone.

You shouldn’t fool yourself into thinking that Dawkins would agree with anything you have said in this thread. You continue to misrepresent him.


I don't misrepresent him - I am referring to his stated opinion about the real processes of evolution - but he may not like the conclusions I draw from them, even if they are logically correct, because it clearly doesn't suit his (or your) philosophical viewpoint.


When DNA is a code - what could truly lead to the development of a code?

your answer
Evolution.


The point I was making, (as opposed to the one you try and put in my mouth again), is that the only mechanism we know of for evolution didn't exist before the multi step DNA process (which actually uses 3 sets of codes), and codes as we perceive them have a strong conceptual element. You may regard that as an illusion because your philosophy doesn't allow you to recognise that possibility at a molecular level - but others like me accept the evidence that there is something more to setting up a code than just chemistry - especially when 3 different codes have to work seamlessly together. I'd like to have some ideas about how that could come about, because the current explanation doesn't cut it.

That explanation doesn't have to be creationism or some religious bogeyman, (as you try to label people you disagree with), but I would like to see if anyone has some ideas about what it might be.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby TheVat on February 4th, 2020, 11:05 am 

I am sorry but that is verging on rubbish. The odds of a single protein emerging by chance are easily calculated, (and have been done so in many books - such as The Origins of Existence by Fred Adams - and I believe Dawkins too). It is a product of the number of types of amino acid components used, the length of the protein chain; and the exact precision of the sequence needed. In short, the authors that I have read, all agree that there are more combinations of amino acid components in one average length protein than there are atoms in the universe. Hence the odds - especially when different randomly emerging proteins have to somehow find each other and work in harmony with each other - presumably by chance as well.


The key is that we don't have to surmount the odds of getting one specific protein but rather the odds of getting any protein. There was no direction towards a specific set of choices. We come from the proteins that happened along and had favorable thermodynamic profiles. And the number of chemically favorable environments, tidal pools and such, was enormous. Akin to that very large room, full of typing monkeys, where Hamlets soliloquy had a fair chance of being typed.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby hyksos on February 4th, 2020, 11:57 am 

lateralsuz » February 4th, 2020, 7:32 am wrote:especially when 3 different codes have to work seamlessly together. I'd like to have some ideas about how that could come about, because the current explanation doesn't cut it.

That explanation doesn't have to be creationism or some religious bogeyman, (as you try to label people you disagree with), but I would like to see if anyone has some ideas about what it might be.


:

hyksos » February 3rd, 2020, 8:14 am wrote:Books worth of ink have been spilt on this topic. Our best educated hypothesis is that it - - -



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Paperback, Second edition, 112 pages
Published September 28th 1999 by Canto/Cambridge University Press (first published February 1986)
Original Title
Origins of Life
ISBN
0521626684 (ISBN13: 9780521626682)
Edition Language
English




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Paperback, 336 pages
Published November 1st 1996 by Oxford University Press, USA (first published 1995)
Original Title
At Home in the Universe: The Search for the Laws of Self-Organization and Complexity
ISBN
0195111303 (ISBN13: 9780195111309)
Edition Language
English




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Hardcover, 339 pages
Published December 5th 2008 by Springer (first published 2008)
ISBN
3540788220 (ISBN13: 9783540788225)
Edition Language
English



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Paperback, 336 pages
Published January 4th 2002 by Basic Books (first published 2000)
Original Title
Signs of Life: How Complexity Pervades Biology
ISBN
0465019285 (ISBN13: 9780465019281)
Edition Language
English
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby hyksos on February 4th, 2020, 12:10 pm 

laterlsuz,

For your convenience, I will now briefly synopsize each of the four authors, so you have a ballpark estimation to help you decide which book to read first. Okay...

Freeman Dyson
The book is super short. Dyson wants to figure out what is means for a collection of molecules to be "alive" and what it means for them when they "die". He wants a definition in terms of physics.

Does Dyson arrive on a conclusive answer? At the book's closing pages, he does not. After reading this book, you will be convinced that science really is missing some crucial piece of the life puzzle.

Stuart Kauffman
Kauffman is the autocatalysis guy. He tends to the overweening side, and blabbers a bit about "God". But he's very much not religious. In any case, the open chapters have Kauffman expressing the deep-seated worry that evolution is not a sufficient explanation for what is observed. Something else is needed...


Horst Rauchfuss
Rauchfuss represents the mainstream in biology. His views are probably most closely aligned with the regular posters at this forum, including all the people expressing frustration in this thread. Rauchfuss is very much concerned with the emergence of the genetic code.

The book shown above is not a pop science book. It is a book on molecular biochemistry. It is so dense, that I never finished it. I could barely read some parts of it. You're going to be reading about RNA World, potassium chemistry, and all the other topics that are very "en vogue" on campus.

Ricard Sole
Sole and Goodwin are two people who publicly announce that evolution is insufficient to explain what is observed in biological entities. So they come from the "something more"-camp. This book however, is mostly aimed at computer science majors and mathematicians. I would assume this probably isn't your cup-of-tea. But it's the best example for showing why there is a concrete conceptual bridge that spans between Chaos Theory and Biology.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Forest_Dump on February 4th, 2020, 12:29 pm 

When it comes to arguments about the long odds, I keep thinking about how long the odds are that you will win the lottery. Almost impossible. And yet several times a week someone wins a fortune. So, the odds may be very much against abiogenesis and yet here we are. Whoda thunk it.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 4th, 2020, 12:30 pm 

In the Blind Watchmaker, Dawkins takes this even further by applying a generous (quick) rate of change to the equation, to say that there isn't logically enough time to generate the first cell in the earth timescales we know of, by simple chance.


Bold by me.

Is THIS the passage you are referring to?

It strings a series of acceptably lucky events (random mutations) together in a nonrandom sequence so that, at the end of the sequence, the finished product carries the illusion of being very very lucky indeed, far too improbable to have come about by chance alone, even given a timespan millions of times longer than the age of the universe so far. Cumulative selection is the key but it had to get started, and we cannot escape the need to postulate a single-step chance event in the origin of cumulative selection itself.


bold by me.

Apart from the fact that, if you mean FIRST CELL in all its current complexity, Dawkins (and I) are not talking about that — as has been repeatedly explained to you — notice that word, ILLUSION? Which you curiously OMITTED? Oh, dear, could you be cherry-picking Dawkins??? Heaven forfend!

Fortunately, I have the entirety of Blind Watchmaker at my disposal. More later. ;-)
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 4th, 2020, 12:43 pm 

When it comes to arguments about the long odds, I keep thinking about how long the odds are that you will win the lottery. Almost impossible. And yet several times a week someone wins a fortune. So, the odds may be very much against abiogenesis and yet here we are. Whoda thunk it.


This is exactly it. Those who argue how vanishingly unlikely it is for humans to evolve, or for life to get started in the first place, are laboring under a misapprehension. This line of argument presupposes that abiogenesis/evolution has a goal — to make humans, or perhaps simple cells, or whatever. But, if it had a goal (telos) that the process was not chancy in the first place. If it has no goal, then “first cell” or “humans” are just fortuitous lottery outcomes among a vast number of possible results. Given such a vast number of possible outcomes, the likelihood of any particular outcome emerging is minuscule — but the likelihood of SOME outcome happening, is guaranteed. Your lottery analogy illustrates this perfectly.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 4th, 2020, 12:56 pm 

Perhaps you should have paid attention to THIS passage in Blind Watchmaker — i.e., not cherry-picked Dawkins.

But the point of our ‘numbers of planets’ argument is that, even if the chemist said that we’d have to wait for a ‘miracle’, have to wait a billion billion years — far longer than the universe has existed, we can still accept this verdict with equanimity.. There are probably more than a billion billion available planets in the universe. If each of them lasts as long as Earth, that gives us about a billion billion billion planet- years to play with. That will do nicely! A miracle is translated into practical politics by a multiplication
sum.


Bold mine.

Well, there goes your misrepresentation of Dawkins. This is why cherry-picking is bad — someone, sooner or later, will call you out on it. Notice, too, Dawkins’s point about untold billions upon billions of trials is exactly the one I made upthread.

More later.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Serpent on February 4th, 2020, 12:59 pm 

It's that pesky perspective again.
How improbable that something so unique as me should ever exist! I'm a miracle.
We each experience the universe with ourselves at its center. We look out at a world of large object near us and ever tinier ones far away. We count past time as leading up to our own present moment and that time is crowded with a history of life all aimed at making us what we are; on the other side, an infinity of expectation and aspiration unrolls before us.
Everything in it must somehow relate to us.
I've found that people in their twenties and thirties are most susceptible to generalizing their egocentricity - I suppose they know more about the other stuff in the world than they did at fifteen, but have not yet lost their conceit of immortality, as they will at forty-five.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 4th, 2020, 1:18 pm 

From The Blind Watchmaker:

Cairns- Smith’s view of the DNA/protein machinery is that it probably came into existence relatively recently, perhaps as recently as three billion years ago. Before that there were many generations of cumulative selection, based upon some quite different replicating entities. Once DNA was there, it proved to be so much more efficient as a replicator, and so much more powerful in its effects on its own replication, that the original replication system that spawned it was cast off and forgotten. The modern DNA machinery, according to this view, is a late-comer, a recent usurper of the role of fundamental replicator, having taken over that role from an earlier and cruder replicator. There may even have been a whole series of such usurpations, but the original replication process must have been sufficiently simple to have come about through what I have dubbed ‘single-step selection’.


Bold mine.

And so, again, here we are. Under this hypothesis, the original replicator that emerged from lifeless matter was crude and simple. Complexity came later. If this is right, the odds of crude replicators arising early by chance and circumstance is, of course, much greater than that chance of complex cells so arising — but this what I have been telling you all along. NO ONE thinks that modern, extremely complex cells arose in single-step selection!

More to come.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 4th, 2020, 2:41 pm 

In Blind Watchmaker, Dawkins goes on to discuss:

Cairns-Smith’s guess is that the original replicators were crystals of inorganic materials, such as those found in clays and muds.


Now I am not going to discuss this clay stuff in detail. I am quoting passages at length from Blind Watchmaker to show how lateralsuz has cherry-picked Dawkins, and completely twisted around his argument about the probability of abiogenesis. Anyone can read the whole book here.

I have been focusing on Chapter Six: Origins and Miracles.

I want to quote this, however, from that chapter, about the clay hypothesis:

Keep holding in mind that there is no suggestion of ‘deliberate’ engineering, either here or in modern, DNA-based life. It is just that the world automatically tends to become full of those varieties of clay (or DNA) that happen to have properties that make them persist and spread themselves about.


Now I do not know what lateralsuz means, exactly, by “control,” because she won’t tell us. I have never claimed that she is an advocate of ID/creationism or religious explanations for the start of life. Very early in this thread, based on the example I linked of the author she herself invoked, I speculated that she believes that molecular or even smaller elements show some kind of rudimentary intent. At any rate, that is clearly what her author (sorry, I can never recall how to spell his name) believes. I don’t know what lateralsuz believes. She won’t say!

But what Dawkins, at any rate, clearly DOES say, is that invoking design, engineering, telos, control, intent, or anything of the sort, for either abiogenesis or evolution, is clearly unwarranted. So forlateralsuz to invoke Dawkins on behalf of her arguments, whatever they actually are, is completely unwarranted.

As Dawkins readily admits, the clay theory of abiogenesis that he discusses is speculative. He goes on to discuss, in greater detail, how to calculate probability estimates — how humans, with their short life spans, have an intuitively different grasp of probabilities than, say, a very-long lived alien species. All of this is an elaboration of what I said upthread. Dawkins agrees with me, not with lateralsuz.

Whether the crystal/clay theory of abiogenesis, or hydrothermal vents, or whatever, is true or not, is beside the point.

The point is that the (numerous) abiogenesis hypotheses are plausible,do no violence to probability estimates, and have no need of “control,” design, intent, or whatever. The burden of proof is not on science to show that any of these hypotheses are true. The burden is on those who claim they cannot be true, and thus we must invoke “control,” “design,” or whatever.

lateralsuz has not even come close to meeting this burden of proof.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Forest_Dump on February 6th, 2020, 10:59 am 

Following from an earlier post, I find a bit of confusion between the matching of questions and the preferred answers so let me try to reorganize a little.

If I wanted to head out into space with my chemistry kit and start life from scratch, based on what science has suggested, there are a number of different formulas and environments I could try to start life but, given the odds and the amount of time it would take, I would probably want a few prayers and/or goats to sacrifice, etc., to shorten the odds. I doubt it would work - I have prayed virtually every time I have bought a lottery ticket and it hasn't worked so far.

However, if I wanted to explain how come we won the lottery of life on this planet, we have lots of good hypotheses already offered. Any one of them could certainly be wrong and it is also possible that the real answer just hasn't been offered yet. But most of them do not require prayers or goats to sacrifice so, since I have no way of assessing what effect prayers or dead goats would have had on that lottery win of several billion years ago, I am not inclinded to take those seriously. But I could be wrong. Now if you have some way of explaining that long ago lottery win (with or without prayers and dead goats) that works better and is more easily understood and evaluated, then bring it on. But I still like the old saying that it is better to light one candle than curse the darkness so if all you want to do is pee on candles than I hope you will forgive me if I more on.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 8th, 2020, 8:24 pm 

The Vat/everyone

I have not yet had the time to read the books suggested by Hyksos, so my comments below are based on my knowledge to date. Equally if I have to find the necessary passages in Dawkins texts then that will slow me down too.

I have never said that that it was impossible for any protein to arise within a short timeframe, because as everyone knows, someone wins the lottery every week. That is not the point. The issue is that a second perfect copy of the same protein cannot be reasonably expected to occur in a viable timeframe to enable any evolutionary process to occur through simple chemical experimentation without a reproductive mechanism, or even to allow trial and error to establish worthwhile interactions with other proteins, (as general chemical activity would be likely to break down the molecular chain before anything useful occurred).

We label polymers as 'proteins' because they turn out to be useful in the context of other proteins and for the operations they achieve - particularly within living cells. Even the most simple cell that we can envisage has many useful tasks to accomplish. If you/others are saying that all of the necessary proteins happened to arise in the same place at the same time by pure chance and without a reproductive mechanism, in order to create the first cell, then honestly, I do not find that credible. Nor do many others.

I can accept that an unknown process may have led to a precise reproductive capability which facilitated an alternate form of evolution, but we have no idea what that might be, and the only process we have for protein reproduction is complex and requires several steps. So it is likely that several different independently arising proteins or other such chemicals would still need to arise by chance to get things going. They would also have to find each other, and work perfectly together before that reproductive mechanism could get going. Those are still very long odds because they are not reflecting a single lottery draw, but a number of them which also have to achieve perfect harmony.

While nature does not have a specific outcome in mind, the capability of achieving perfect protein reproduction by any means is, because it is necessary for what must logically follow.

The only reproductive method that we do know about involves a highly complex set of process which use several coded interactions. The coding makes the concept of what we have to achieve significantly more challenging.

While people have speculated that life could have emerged anywhere in the universe, as a way of extending the size of the experimental field, the distances involved and the extreme cold that would have to be overcome to get that living cell here are not conducive to transportation of that nature. It is again not credible.

As things stand, and with the evidence available, I personally feel that life had to emerge here. The question is how? The factors I have mentioned are not fanciful and should be taken seriously if the world is to be persuaded by any explanation.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby TheVat on February 8th, 2020, 9:04 pm 

Lateral, thanks for sticking with us and giving your clearest statement of the arduous conceptual journey from chaotic chemistry to coded protein replication. In a perfect world, we would all have time and the prerequisite knowledge to read Rauchfuss, Sole, et al. And have mastered chaos theory. I have a background in life sciences, and still find this all mindbending in its difficulty. I share the skepticism regarding the Panspermia theory, though I wouldn't rule out the possible hardiness of some spores, especially embedded in rocky ejecta.

More daunting is the question of complex proteins "finding each other" and maybe someone here (David?) (Hyksos?) can help us get a better handle on assessing probabilities. Wherever it happened in the universe, certain steps had to happen THERE, and in proximity. You make a reasonable point, AFAICT, that any early RNA world involves multiple lottery wins that harmonize in some fashion.

Also, I apologize for an ill-considered joke (and it was just a joke) I made earlier regarding this forum's aversion to New Age flakiness. While it is true that Gwyneth Paltrow does sell candles that she claims to have the scent of her nether regions, it was a bit too crude of an example to use in what was intended as a light remark. I have no excuse.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 8th, 2020, 10:15 pm 

Fred really sucks at darts. When Fred throws darts, he makes a bull’s eye 1 in 1,000,000,000,000 throws.

Given how badly Fred sucks at darts, how many bull’s eyes do you think Fred will make if he throws darts an infinite number of times?

Design Inferences in an Infinite Universe, by Bradley Monton
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Serpent on February 9th, 2020, 1:44 am 

lateralsuz » February 8th, 2020, 7:24 pm wrote:I have never said that that it was impossible for any protein to arise within a short timeframe, because as everyone knows, someone wins the lottery every week.

Sure, but what are the odds of the winners knowing one another? Well, that depends. If only a thousand tickets are sold in a nation of millions, quite poor. If the same thousand tickets are sold in a single town of 4000 residents, pretty damn good.
That is not the point. The issue is that a second perfect copy of the same protein cannot be reasonably expected to occur in a viable timeframe to enable any evolutionary process to occur through simple chemical experimentation without a reproductive mechanism, or even to allow trial and error to establish worthwhile interactions with other proteins,

Each step doesn't have to wait for a single once-in-a-blue-moon chance occurrence. Start with a medium - a nice, rich, concentrated primordial soup, at just the right temperature and pH, and you might have protein molecules forming longish chains every minute. In close proximity, where they can't help bumping into one another repeatedly. Now add a good energetic thunderstorm with frequent lightning strikes.
Most of the accidental molecules still won't come alive. But if, once in ten thousand years, blind luck produces a stable compound - one that resists random breakage or dissolution in water - that one doesn't have to wait for that same long-shot to find another molecule to bond with: it already has lots of small molecules jostling around, and lots of bonding points for those little molecules to glom onto. Like a smelly, squishy version of chrystal formation.
The thing just keeps growing, and the bigger it gets, the more elements it collects, the more complex it is, it becomes more complex. It keeps growing until something changes. The pause between lightning strikes stretches to two minutes, loose oxygen atoms outnumber hydrogen atoms, the temperature drops one degree - some little thing changes.
This is when you find out whether your macromolecule is alive. When conditions change, does the giant polymer a. just sink to the bottom and lie there b. start fragmenting c. migrate toward more favourable conditions, d. break up into just two mirror-image polymers, like opening a zipper? Cose that would make bonding sites available to loose atoms that have the requisite properties and that's replication.
It's nowhere near "useful" yet. It just resists unbecoming.
From that point, you don't need the infinite blind guesses anymore: you have a template that retains its pattern and can repeat that pattern - given only that the materials and conditions remain largely favourable with just enough fluctuation to elicit a response.

If you/others are saying that all of the necessary proteins happened to arise in the same place at the same time by pure chance and without a reproductive mechanism, in order to create the first cell, then honestly, I do not find that credible.

They didn't have to "arise" at the same place and time. They could have formed individually, been washed around, settled and got stirred up again, millions of times over millions of years before there was so much as a whiff of a cell. Just lumps. Then the lumps lucky enough to have captured a stray phosphorous held up over the next million years a little better than the ones that had a bromine in the same position...
I don't know the exact chemistry; I'm just making up a narrative.

Thing is, once accident/chance has produced something that works, that thing keeps working. It doesn't need to find the right other bits to do something in particular: whatever bits happen to be available interact in the patterns determined by their configuration. It doesn't "have to achieve" anything. Proteins never meant to become a cell or reproduce or grow into an alga, an albatross or an alligator ... that's just how things turned out.

The factors I have mentioned are not fanciful and should be taken seriously if the world is to be persuaded by any explanation.

Why should we need to persuade the world that life started?
It's alive. It's here. Get used to it.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 9th, 2020, 12:42 pm 

Lateralsuz,

The a posteriori probability of life arising on earth is 100 percent. The a priori probability of it doing so is unknown. Therefore, all your probability arguments are null and void.

If you/others are saying that all of the necessary proteins happened to arise in the same place at the same time by pure chance and without a reproductive mechanism, in order to create the first cell, then honestly, I do not find that credible.


No, we are not saying that. This is a STRAWMAN. Read what Serpent just wrote. Better yet, actually READ the long list of abiogenesis models I gave you, and read the proposed abiogenesis model proposed by Dawkins in The Blind Watchmaker. You implied that you read the book, but, as I have shown, you cherry-picked his claim about the possibility of life getting started, took it completely out of context, and changed his meaning to the precise opposite of what he intended!

This is the exact same mistake that Behe makes with his stupid “irreducuble complexity” argument about flagellum. According to him, all the “irreducibly complex” components of a flagellum must fall together at the same time, miraculously, against all feasible probability estimates, for the flagellum to exist. In reality, the flagellum evolved in a stepwise process featuring exaptation, in which components previously adapted for other functions were commandeered for new functions. Life no doubt started the same way — not everything needed for the first simple replicators had to miraculously fall together at the same time. They did so sequentially, each step commandeering a previous step. Again, please READ Dawkins — his whole book is online, and I linked to it earlier.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 10th, 2020, 8:45 am 

Hi Serpent

Sure, but what are the odds of the winners knowing one another? Well, that depends. If only a thousand tickets are sold in a nation of millions, quite poor. If the same thousand tickets are sold in a single town of 4000 residents, pretty damn good.


I think your scale is somewhat adrift. We are not talking one in 4,000, or even one in 4 million. Every protein, (or RNA equivalent), has odds which are in the billions of trillions.... more combinations than there are atoms in the universe.

We also have to have several of them together - which requires 'multiple lottery draws', and they have to work together perfectly.

You have also made the point that the odds were overcome because we are here. Yes, but how? There is nothing to say that it was by chance alone. That is just your chosen philosophy. I believe in process as a way to achieve life, but we don't know how. It could be very important.

On your own principles, it is undeniable that the method of reproduction which nature emerged with was using multiple codes working in harmony.

I know this is inconvenient to your philosophy, but it is still there as a fact that has to be explained.

Now add a good energetic thunderstorm with frequent lightning strikes.


What on earth has that to do with anything related to the above? There is nothing that a thunderstorm could do to shorten the odds.

Most of the accidental molecules still won't come alive.


Wow - a chink in your armour! Even I don't say that individual molecules are alive.... and how do you define alive?

But if, once in ten thousand years, blind luck produces a stable compound - one that resists random breakage or dissolution in water - that one doesn't have to wait for that same long-shot to find another molecule to bond with: it already has lots of small molecules jostling around, and lots of bonding points for those little molecules to glom onto.


Scale again. Try a few billion years for chance alone.
Beyond the time factor, in a turbulent early solar system, and possibly a planet that has only just cooled I simply do not believe that fragile protein molecules will be able to hang around for long periods, untouched, waiting for the perfect partner molecule to arise.


This is when you find out whether your macromolecule is alive. When conditions change, does the giant polymer a. just sink to the bottom and lie there b. start fragmenting c. migrate toward more favourable conditions, d. break up into just two mirror-image polymers, like opening a zipper?


Wow - a single living macromolecule now!

From that point, you don't need the infinite blind guesses anymore: you have a template that retains its pattern and can repeat that pattern - given only that the materials and conditions remain largely favourable with just enough fluctuation to elicit a response.


And where does this miraculous capability come from? We see no examples of complex molecules recreating themselves. The mechanism we have is for a ribosome (complex in itself), to construct a protein from an RNA template.... 3 sets of codes. Codes.

Why should we need to persuade the world that life started?
It's alive. It's here. Get used to it.


Because you do have to be credible.
I am used to the facts we have discovered about life, thank you. I feel you should address them too. Codes.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Serpent on February 10th, 2020, 10:11 am 

You have also made the point that the odds were overcome because we are here.

How do you know?
Never mind - I wouldn't be able to understand it.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 10th, 2020, 10:59 am 

I think your scale is somewhat adrift. We are not talking one in 4,000, or even one in 4 million. Every protein, (or RNA equivalent), has odds which are in the billions of trillions.... more combinations than there are atoms in the universe.


Read Dawkins. This is his argument , which you mischaracterized. He explains why your illusion is invalid.

We also have to have several of them together - which requires 'multiple lottery draws', and they have to work together perfectly.


Did you even read my last post? Did you read Dawkins on clays? These multiple lottery draws do not have to happen at the same time. They can happen sequentially, over many, many draws over millions of years, each new draw added incrementally onto the result of the previous draw. This is basic stuff that you either do not understand, or else refuse to.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 10th, 2020, 11:41 am 

While people have speculated that life could have emerged anywhere in the universe, as a way of extending the size of the experimental field, the distances involved and the extreme cold that would have to be overcome to get that living cell here are not conducive to transportation of that nature. It is again not credible.


No, this NOT what Dawkins is saying. You do not need panspermia — he isn’t arguing for that. What he is saying, correctly, is that if you want to estimate the number of trials needed for life to arise somewhere, anywhere, by, as he put it, “a happy chemical accident” — then you must consider not just the trials on earth, or on any particular planet, but ALL the trials, on ALL the worlds, the full ensemble of worlds in the universe. If the universe is spatially infinite, as evidence suggest that it is, then, as Monton pointed out in the paper that I linked, we should except there to be an infinite number of inhabited planets, by happy chemical accident alone, no matter HOW rare life is. A minuscule subset of infinite is still, itself, infinite. You cannot use the argument to “number of atoms in the universe,” if that number is infinite.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby davidm on February 10th, 2020, 11:58 am 

Please address your mischaracterization of Dawkins. You wrote:

In the Blind Watchmaker, Dawkins takes this even further by applying a generous (quick) rate of change to the equation, to say that there isn't logically enough time to generate the first cell in the earth timescales we know of, by simple chance.


Dawkins ACTUALLY wrote:

It strings a series of acceptably lucky events (random mutations) together in a nonrandom sequence so that, at the end of the sequence, the finished product carries the illusion of being very very lucky indeed, far too improbable to have come about by chance alone, even given a timespan millions of times longer than the age of the universe so far. Cumulative selection is the key but it had to get started, and we cannot escape the need to postulate a single-step chance event in the origin of cumulative selection itself.


And …

But the point of our ‘numbers of planets’ argument is that, even if the chemist said that we’d have to wait for a ‘miracle’, have to wait a billion billion years — far longer than the universe has existed, we can still accept this verdict with equanimity. There are probably more than a billion billion available planets in the universe. If each of them lasts as long as Earth, that gives us about a billion billion billion planet- years to play with. That will do nicely! A miracle is translated into practical politics by a multiplication sum.


All bolds by me.

Again, in invoking the entire ensemble of worlds, he is NOT invoking panspermia, but correctly pointing that you need to include trials on ALL worlds, not just ONE world, in talking about the probability of abiogenesis on ANY world.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby lateralsuz on February 13th, 2020, 5:23 am 

davidm

I don't know why you remain fixated on trying to prove some abstract point about what words Dawkins chose to use.

You have admitted that Dawkins doesn't deny the maths I have stated.
What you say is that Dawkins, (like me - stated many times), believes in a process that largely eliminates the odds.

If there is no dispute about this, why are you going on about it?

I also agree that Dawkins is not necessarily saying that life had to be transported here. He primarily believes that if life could arise statistically from the larger melting pot of the Universe then wherever it arose it would seem miraculous. He is, (like me), agreeing that life had to start here from a process.

Again - what's your point?

My point is that if it has to arise here, the odds still have to be overcome somehow - by a process. But as things stand, they remain big odds, because (as Dawkins admits) we have a limited timeframe due to the age and circumstances of our planet.

The mechanisms of a chance encounter are still driven by the scientific principles that we know, concerning how chemicals interact. Various people (Fred Adams and Christophe Finipolscie being two of them) show that the window of opportunity, (after the earth had cooled sufficiently), was somewhere between 100 and 200 million years. That is a very narrow window.

From what we imagine, that environment would also be highly chemically reactive and therefore highly unlikely to allow long amino acid chains to remain undamaged for long periods, or even relatively short ones, before being chemically broken down. So we have a conceptual challenge which Dawkins also admits, as you quote above.

Dawkins' choice of words plays this down, but the facts don't go away. A replicator of complex cells had to emerge, and the ONLY mechanism which we know of, (which was the one that did emerge), is highly complex and relies on 3 sets of codes - another thing which Dawkins acknowledges but doesn't address.

A ribosome is highly complex, and from what I read, there are 3 types - each dedicated to one of the 3 core types of living cell. Until recently these 3 types of ribosome had no perceived evolutionary path between them - either to indicate a common ancestor, or that two permutations emerged from an original. This also implied that the highly complex molecular components were not a permutation of a single chemical chain but the core of the long odds issue.

To try and overcome such an fact, some scientists have been almost desperate to find an earlier evolutionary mechanism - and without managing to do so, have instead been looking for clues which might suggest that one existed, (presumably to preserve their funding). The only thing they have come up with is that they see some common sections of protein/RNA code in some of the component parts of a ribosome. But in truth, this is still just a hope by some scientists who try to limit the odds of achieving this core component of life before the first cell existed - the cell that would seem to give it purpose... although 'purpose' would not be a part of of a theoretical evolutionary mechanism as we understand it, (based on chemical interaction alone).

Your own quote from Dawkins acknowledges that the starting point had to be by chance - but the thing he doesn't state is how long the odds remain.

When looking for a process to shorten the odds, we also have to accommodate the emergence of codes - a conceptual factor that is not normally considered to be a matter of chance. They do affect our perception of an evolutionary process and they either add massively to the odds based on chance processes, or we have to identify another influencing factor - whatever that may be.

So will you please address the issues we have been trying to make.
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Re: Evolution : a process of ‘change’ not of ‘start’

Postby Serpent on February 13th, 2020, 11:15 am 

Abandon hope. Our existence is impossible.
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