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Theories - Origin of Life

Discussion of everything related to the Theory of Evolution.

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Re: Theories - Origin of Life

Postby wbla3335 » Wed Dec 21, 2011 2:40 am

scottie wrote:I would argue that providing evidence from Scientific journals and peer reviewed scientific papers strengthens my position. The fact that you don’t regard this as recognisable support I find rather surprising.

If the proportion of the "evidence from Scientific journals and peer reviewed scientific papers" that supports your position were more than tiny, your position might be a bit stronger.
As I said earlier,
wbla3335 wrote:Every opinion under the sun can be found on any topic imaginable.

And some of it gets published. Publication guarantees nothing.
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Re:

Postby JackBean » Wed Dec 21, 2011 7:01 am

So far, although you were bullshitting with non-sense, I have respected you at least because you were stick with your opinion, no matter, how silly it may be. But I see, you are neglegting yourself already.

about14351-336.html
JackBean wrote:scottie, I'm sure you will first answer my very old question, right?

JackBean wrote:You have not again said, how did the humans appear on Earth. Try to read this carefully and pick one possibility (or come up with other, but do not start about lysosomes :roll:)
1) they were created when all the other life on Earth was created few billions of years ago
2) they were created few tens/hundreds thousands of years ago when the creator was bored again and had no forum to post on
3) they evolved from lower animals, no matter, whether these were created or arose spontanneously


you said, that 1 and 3 are wrong, so the creator "arrived" several times on Earth and worked on schifts, right? That would at least explain, why we don't find fossils of recent animals in say Mesozoic era.

scottie wrote:Jackbean

The No 2 option of yours is the nearest to my view without of course the rather silly appendage you have attached.


Another thing you have not responded to:
JackBean wrote:The simple question is this.
Is intelligent design actually supported by evidence or is it simply your belief that it is.

Since you require evidence for evolution, how is that, that you do not require one for ID?


scottie wrote:
Right, they are all wrong, all the evolutionists, all IDers and all creators are wrong, but one retired engineer with no biological knowledge is right


My major point seems to have escaped your understanding.

If evolutionary theory (in all it’s various forms) is correct then there will be no disagreement between the theorists as to what the mechanism that drives macro evolution actually is.
The reality that different dissenting views not only exist but are actually competing for prominence demonstrates that the mechanism is not known.
The only common thread that unites the various adherents is that a naturalistic cause is the only one that is acceptable, regardless of where the evidence leads.

This makes any of these theories philosophically based. That is not a view I have any difficulty with, other than the point that it is regarded as a scientific fact and any dissension from that view is regarded as intolerable and therefore worthy of censorship, as you yourself have so plainly demonstrated.

Imagine, that we are able to travel in time and transfer say a car into medieval times. They will try to explain, how the car functions, but none of them will be probably right, since they don't have enough knowledge. Does that mean that the car doesn't work?
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Re: Theories - Origin of Life

Postby scottie » Wed Dec 21, 2011 10:30 pm

Jackbean is on one of his rants again so I will just patiently wait for him to calm down

awkko808

It is such a pleasant change to discuss this matter in a rational way and for that I do sincerely thank you.
Actually I agree with just about everything you have said,only to comment on your last sentence.

It seems, with respect, insignificant to argue over whether a designer exists, at least with current human knowledge of the physical world.


You are right in what I have been trying to do, that is to point to the empirical evidence that shows how unsupported Darwinian theory is.

I fully realise that this attacks the very core belief of many, hence the philosophical noise that is generated toward me.

You so rightly say that science encompasses both logic and empirical evidence.
What I have been doing is presenting empirical evidence against the Darwinian mechanism of speciation, not the logic of it.

Logically a designer could quite rationally have set in train the Darwinian mechanism.

The problem is ---- Does the empirical evidence point in that direction?

Lenny Moss puts this far better than I can
Once upon a time it was believed that something called “genes” were integral units, that each specified a piece of a phenotype [that is, a trait], that the phenotype as a whole was the result of the sum of these units, and that evolutionary change was the result of new genes created by random mutation and differential survival. (Moss 2003, p. 185)


Question—Has that belief been supported by the empirical evidence.

The comparative genome analysis of the Human Genome project has produced some unexpected results.

Lets take just one strand of evidence from the picture that has emerged

Non coding (so called Junk) DNA accounts for only 10% of a one celled prokarote,
only 32% in yeast,
75% in roundworms,
83% in insects,
91% in a pufferfish.
Costa, Fabricio F. (2008). "Non-coding RNAs, Epigenetics and Complexity", Gene vol. 410, pp. 9-17.

Most of the human DNA (some 98%) does not code for proteins.
The bulk of this non coding DNA was referred to as junk i.e. the evolutionary accumulation of meaningless genetic leftovers.
This was a central argument from the likes of Dawkins, Coyne and others and cited as as a main line evidence of random Darwinian evolution.

However it now appears that the more complex the organism the greater is the amount of this “junk”.
This is highlighted in this paper
The relationship between non-protein-coding DNA and eukaryotic complexity
http://onlinelibrary.wiley.com/doi/10.1 ... 4/abstract
We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases consistently with complexity. We also show that the distribution of introns in complex organisms is non-random.


The above is a direct quote from the above abstract and this evidence is the direct opposite of what was believed to be true, based on Darwinian theory.

Notice also that these intron distributions are non random.
Now this is some the evidence from the non protein coding part of the genome.

What about the other book end--- the protein coding part.
Once upon a time it would have stood to reason that the complexity of an organism would be proportional to the number of its unique genetic units. (Moss 2003, p. 185)

Well it was first expected that the Human genome would contain about 100,000 genes.
Now why would a figure around 100,000 be expected?
Simply because a tiny roundworm has about 20,000 and humans are clearly much more complicated, therefore the, one gene one trait, concept that our good friend Mr Dawkins contended, had to predict much more than in a simple roundworm.

This project has revealed our genome to contain only about 23,000
But that is not all.
Recently researchers have found that a pea aphid has about 34,600 genes and better still, that the water flea has 39,000 genes.

How does Darwinian theory explain this?
Well it can’t because the evidence requires a completely different principle of causation.

The only other causation I am aware of is design by some outside agency.
( Craig Venter has demonstrated the principle of that concept.)

If there can be another cause that explains this evidence then it should be explained rather than clinging to a causation that clearly isn’t supported by the empirical evidence.

You have quite rightly pointed to areas of evidence that can be examined and all I have done is examine some of that evidence (there is a lot more) and report on it.

Who or what the designer may or may not be is a question that science cannot answer at this point, because that cause appears to sit outside our physical laws.
Defining or trying to understand that cause is a philosophical/religious question that the physical sciences cannot engage with except that scientists have the humility to acknowledge that, as indeed many do.
Sorry for such a long post.
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Re: Theories - Origin of Life

Postby wbla3335 » Thu Dec 22, 2011 12:01 am

scottie

I believe you have somewhere accused scientists of neglecting supernatural influences. Well, you are right. Scientists must do this. Science would have no power if they didn't.

http://weber.ucsd.edu/~aronatas/project ... e.3.12.htm

Concluding the existence of a supernatural cause of anything by an analysis of the evidence amassed by the sciences is untenable. What is tenable is the desire to justify a preconception by selective interpretation. Your strategy is the same as that used by creationists: ignore or discount the majority of human knowledge and try to hammer the remaining minority into the square hole of what you want to be true. I have no problem for you to believe whatever you want (since you don't seem like the type who wishes harm to those who don't share your views), but you are unlikely to win any converts on this particular forum.

You almost sound like someone in transition - raised Christian, intelligent enough to see the absurdity of a theist god who helps certain teams win football games, but sufficiently indoctrinated against the purposelessness of a natural universe. May you continue your journey. As someone said earlier, we all take leaps in choosing what we believe. Some leaps involve probabilistic extrapolation from the known, some involve faith. Scientists, by their nature, choose the former. Theists and deists, by their nature or parents (usually the parents), choose the latter.

I hope to see you on the "other side" some day.
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Postby JackBean » Thu Dec 22, 2011 8:11 am

scottie, I think you want to answer before I "calm down"
http://www.biolib.cz/en/main/

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Re: Theories - Origin of Life

Postby canalon » Thu Dec 22, 2011 7:39 pm

Scottie

Would you please answer on your position on double standard when it comes to proof?

Professor David Dreamer of Ohio State University has investigated this subject and you can find his paper entitles ENTROPY AND CAVE ANIMALS here
https://kb.osu.edu/dspace/bitstream/handle/1811/5008/V64N03_221.pdf?sequence=1
This is how he commences his paper (just to whet your appetite)
It is generally accepted that these animals are descendants of eyed and pigmented ancestors. Since this trait is so widespread among cave animals, any explanation of its evolutionary mechanism must also account for its ubiquitous occurrence. A number of hypotheses have been offered but it remains something of a problem for Darwinian theory

He concludes with a proposal that has to move away from Darwinian natural selection to make a reasonable case, that interestingly can be applied to the design view as well.


You have noted that this paper is dated from 1964, and that since then our understanding on how evolution works has slightly changed. Even if the Darwinian idea is still at the core of the theory of evolution, there are plenty of things that have been better understood and explained with respect to mechanisms and the implication of genetics. This paper has become largely irrelevant because it simply ignores what molecular biology has discovered since it was published. I do not blame the author for that, but using it as a support for your own theory only demonstrate your total and utter lack of understanding of the subject at hand :roll:
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
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Re: Theories - Origin of Life

Postby awkko808 » Fri Dec 23, 2011 1:36 am

scottie,
Thank you, rationality is the only way to solve these debates. It is a hot topic but I see no reason in losing rationality over this debate. In fact, I do believe there is good possibility for your beliefs to be true based on the number of sources from which you have drawn support for your argument. I actually took some time to read over Deamer's article because upon skimming it did pose some challenging points. Upon further reading however I could see I wasn't convinced. Although I am no expert in animals, especially cave animals, I don't agree with it much because of several specific problems:

First of all, one of Deamer's underlying premises seems to be that natural selection is goal-directional, through which life should move from simple to complex. I believe this is an error, as natural selection implies that any organism, simple or complex, able to survive in an environment has a better probability of generating offspring with its genes. Technically, degenerate evolution would be very possible through natural selection, but this doesn't happen very often because the loss of sensory organs suggested by Deamer would usually be detrimental in nature. What Deamer hypothesized was that degenerate evolution would be possible in a lab environment, and I believe it would be possible. But of course that wouldn't be NATURAL selection now would it?

From Deamer's article:
It is generally accepted that these animals are descendants of eyed and pigmented ancestors. Since this trait is so widespread among cave animals, any explanation of its evolutionary mechanism must also account for its ubiquitous occurrence. A number of hypotheses have been offered but it remains something of a problem for Darwinian theory.


I believe what you are arguing is that multiple analogous adaptations pose a problem for Darwinian theory. As I mentioned above, natural selection has no bias with respect to degeneracy. If it works, it works. I believe that over long periods of time, which is what Darwinian theory is partly based on, it would be possible to see such analogous adaptations. This is where I believe faith comes into play, because I have absolutely no idea what could realistically happen over such long periods of time, or "deep time" as some would call it. Perhaps the real argument against Darwinian theory should be on whether such changes can occur over vast periods of time.

To carry the argument further, if very small decreases in energy expenditure did have positive survival value in caves, it would seem likely that evolutionary processes would produce cave animals which are miniaturized versions of corresponding species aboveground. However, in my experience the size ranges are not drastically different.


Another problem is in this argument. Deamer rebuts Rhoades's suggestion that, given a cave environment, eyes would be lost in cave-dwelling organisms because of the minute energy costs required to maintain eyes. Deamer goes on even to say that if energy expenditure was a problem for cave-dwelling animals, then they would eventually shrink. This is erroneous because for cave-dwelling animals to "shrink" they would have to lose some adaptations, and this would be disadvantageous to their survival. This is from what I'd speculate, however, because I am no expert in cave animals.

There were no selective processes going on to preserve strains with vision and pigment. Therefore, randomization of the genetic information could occur through mutation without destroying the survival potential of the species and naturally the system would proceed to the maximum entropy possible. This would result in totally eyeless and unpigmented species of animals.


What he did here was compare a process that probably occurred in cave animals to a process that probably occurred in the rest of the animal kingdom. As I mentioned above, degenerate evolution could very well be possible through natural selection but it doesn't happen in nature.

The point, I guess, is that Deamer is taking a few bits of Darwinian theory and trying to explain it in a lab environment. But Darwin's mechanism of natural selection, as its name might imply, takes place in nature.


scottie:
Well it was first expected that the Human genome would contain about 100,000 genes.
Now why would a figure around 100,000 be expected?
Simply because a tiny roundworm has about 20,000 and humans are clearly much more complicated, therefore the, one gene one trait, concept that our good friend Mr Dawkins contended, had to predict much more than in a simple roundworm.

This project has revealed our genome to contain only about 23,000
But that is not all.
Recently researchers have found that a pea aphid has about 34,600 genes and better still, that the water flea has 39,000 genes.

How does Darwinian theory explain this?


The relation you hold here is that an increase in the NUMBER of genes is an increase in the complexity of an organism. I'd argue that the number doesn't attribute completely to the complexity of the animal. More important factors, aside from the amount of genes, is how the organism expresses it, and WHEN it expresses the genes. To be more specific, there are certain developmental genes I have heard of that are expressed at distinct stages of the organism's development and SMALL changes in the genes can lead to LARGE changes in the organism's morphology. Although I'm sure there are more that exist, the only genes I have been taught about are the Hox genes, commonly studied for their effects on segmentation in Drosophilia.

You'd also ask how the increase in noncoding DNA ties in with this. Well, since a good number of noncoding DNA sequences have been known to REGULATE DNA and thus gene expression, we can speculate that the increase in noncoding DNA may correlate to an increase in regulation mechanisms in humans that allow certain genes to be expressed at precise times allowing for particular physiological functions to happen. Thus, it seems plausible that not only do the number of genes factor into the complexity of an organism, but also the manner (i.e. how much they are expressed) in which they are expressed and when they are expressed. Just because humans have less coding genes doesn't mean they're less complex.

I also apologize for the long post. The larger the post, the more likelihood of error it seems.
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Re: Theories - Origin of Life

Postby Dov Henis » Fri Dec 23, 2011 7:29 am

EarthLife Genesis@Aromaticity.H-Bonding


A.
Purines and pyrimidines are two of the building blocks of nucleic acids. Only two purines and three pyrimidines occur widely in nucleic acids.

B.
Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring.

A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature.

Aromaticity ( Kekule, Loschmidt, Thiele) is essential also for the Krebs Cycle, for energy production.

(Wikipedia)

C.
Natural selection is E (energy) temporarily constrained in an m (mass) format.

Natural selection is a universal ubiquitous trait of ALL mass spin formats, inanimate and animate.
Life began/evolved on Earth with the natural selection of inanimate RNA, then of some RNA nucleotides, then arriving at the ultimate mode of natural selection – self replication of RNAs. ALL Earth life is evolved RNAs. The drive and purpose of EarthLife is to enhance RNAs replication, its natural selection.

Aromaticity enables good constraining of energy and good propensity to hydrogen bonding. The address of EarthLife Genesis, of phasing from inanimate to animate natural selection, is Aromaticity. Hydrogen Bonding.

Dov Henis (comments from 22nd century)
http://universe-life.com/
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Re: Theories - Origin of Life

Postby scottie » Fri Dec 23, 2011 3:25 pm

wbla3335
scottie
I believe you have somewhere accused scientists of neglecting supernatural influences.


You will not find that I have anywhere, said that nor have I made any such accusation. I appreciate you used the word “believe” which only goes to show that beliefs can be wrong. :)

What I have said, and here I paraphrase the summation of all my posts

Scientists should not stray into matters that involve the unnatural or supernatural. Scientists must try and explain matters within the known physical laws.
Explanations beyond physical laws are philosophical.

When the evidence does not support a physical hypothesis then that should be recognised and acknowledged.

Now I do not know of any physical process that can explain the origin of life except that life has only been known to originate from another pre existing life.
That is what science does testify to.

I also do not know of any physical process that can change one species into another quite different species. (definition of species can of course be quite arbitrary.) let’s use this forums definition.
http://www.biology-online.org/dictionary/Species

I do know that within existing species, variation can and does occur and depend on genetic environmental and dietary factors.

I know of only one example where known physical processes have been used to produce a new species. That is the case where an outside agent has, albeit crudely, designed and changed one life form into another. I of course refer to the Craig Venter team.
No doubt others will follow. They have not created a new life, but simply changed and existing life form into another.

As I understand it the smallest unit of a species is a single cell as is also the smallest unit of a life.
I therefore maintain that any attempts to understand how life arose also by definition would understand how species arose.

I am not aware of any physical process that can or has caused a prokaryote to change into a eukaryote.

Finally I do not know of any physical process that can attach symbolic meaning to any chemical molecules that exist in the various genetic codes that life processes utilise.

I think that pretty well sums up my understanding of where science is at this time on this subject.

Since you started off your psychological analysis of me with an incorrect belief, would you mind terribly if I reserve my judgement on it. :)
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Re: Theories - Origin of Life

Postby scottie » Fri Dec 23, 2011 3:39 pm

canalon
Cave animals
You have noted that this paper is dated from 1964, and that since then our understanding on how evolution works has slightly changed. Even if the Darwinian idea is still at the core of the theory of evolution, there are plenty of things that have been better understood and explained with respect to mechanisms and the implication of genetics. This paper has become largely irrelevant because it simply ignores what molecular biology has discovered since it was published. I do not blame the author for that, but using it as a support for your own theory only demonstrate your total and utter lack of understanding of the subject at hand


Patrick oh Patrick, you offer such kind words of encouragement, what can I say? :) How about starting here

Yes the paper is from 1964.
1) Has it been refuted? If so please provide me with a source.
2) Simply stating that our understanding of evolution has slightly changed is just a statement. Could you please explain in what way has it changed to make this paper irrelevant?
3) You don’t blame the author for that but you blame me. That is a delightful little bit of “shoot the messenger” rhetoric.:)
4) The argument though is that vestigial organs militate against functional design. If they are vestigial then they must have had a use initially, therefore this is an argument for degeneration or atrophy, not one against design. It seems you don’t fully understand the nature of this argument.
5) According to Darwinian theory Natural selection is the force, that selects for survival from existing functions. Random mutations are the creative force in Darwinian theory. Since these organs are not necessary for survival Natural selection is not the driving mechanism for their loss. That driving mechanism is a function of increasing entropy and is not a Darwinian mechanism. That is the point Professor Deamer is making.
6) Rhoades (1962) legitimately argues that since less energy is required this make for better survival, hence Natural selection is the force.
7) Deamer counters his argument that this should mean that the cave animals are smaller than the corresponding above ground species, but in his experience there is no appreciable difference in size. He then goes on to cite Vandel (1961) that shows in the case of the blind salamander, in the laval stage, eyes are there and then disappear with maturity. Hope that helps you better understand the principles of Deamer’s paper.
8) btw I have emailed the professor and hopefully will get a response. I will keep you informed, so we can all update our understanding.
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Re: Theories - Origin of Life

Postby scottie » Fri Dec 23, 2011 3:48 pm

awkko808

May I refer you to my response to Patrick where I explained my understanding of his paper.

I fully note your comments however can we put this in abeyance until I perhaps get a reply from Professor Deemer

So to your response
The relation you hold here is that an increase in the NUMBER of genes is an increase in the complexity of an organism. I'd argue that the number doesn't attribute completely to the complexity of the animal. More important factors, aside from the amount of genes, is how the organism expresses it, and WHEN it expresses the genes.


Sorry I should have been a bit clearer, I was not expressing my view, I was expressing the view of the researchers. Perhaps if I cited a reference it would have been clearer.
http://www.ornl.gov/sci/techresources/H ... mber.shtml

The rest of your paragraph I totally agree with.

The point I was making was that evolutionary theory was positing that the increase in complexity was a random happening of the mutation of existing genes, and thereby complexity of phenotype was a result of a greater variety of mutated genes.
We now know that is not the case.

We also now need to ask the additional question.

Since random mutation is the creative force, with natural selection being the selective force
How does this creative force change, not only the function of the genome, but also how the individual genes are expressed, and again when they are expressed?
And even more than that how is the ever changing growth trajectory of the embryo is managed by this random process.

Natural selection has nothing to do with this process. It only comes into play when the environment can act to select one of these changes once they have taken place, to an advantage.

And of course the more complex the organism the more complex these coordinated series of changes have to be.

Now everyone is just making the assumption that this can happen, but the improbability (now I don’t wish to go into the theory of probability) of this is so great that even the theory itself recognises it.
Why else is common decent the other fundamental pillar.
Because it only happened once, says the theory.

It is this creative force that I keep challenging.
Science advances in a culture of doubt.

Your second paragraph I agree with.
The more of this so called junk the more regulated is the organism.
But this junk DNA was being (and indeed in some quarters) still being offered up as the refuse of evolutionary processes and was and indeed still is put out as an argument against design.

Now there is more to this junk question but may I leave that to another post.
RSS is now overcoming me. :)
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Re: Theories - Origin of Life

Postby EnricoPallazzo » Fri Dec 23, 2011 8:02 pm

Hello,
I stumbled over this vivid discussion and cannot resist to interfere...

scottie wrote:[
Yes the paper is from 1964.
1) Has it been refuted? If so please provide me with a source.
2) Simply stating that our understanding of evolution has slightly changed is just a statement. Could you please explain in what way has it changed to make this paper irrelevant?


I think you do not understand the basic concept of schience at all. Wikipedia.com puts it into a nice phrase: "Science (from Latin scientia, meaning "knowledge") is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe." Its all about progression! Scientific data are constantly generated, expanded, revised and sometimes dismissed or refuted. You simply cannot take a single paper, especially an old one, for absolutely granted and ignore all the scientific knowlegde that has been generated since then (what a christian attitude!). That doesn`t make old papers "irrelevant", but in the light of new discoveries quite often much more reasonable explanations can be given for many phenomena. In fact, thats what canalon already tried to explain to you. If you really want to learn about a topic, read recent literature (e.g. reviews).
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