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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 scottie » Wed Feb 22, 2012 8:12 pm

wbla3335

You should not misjudge why I have not taken up on the details of your assertions on NS.
You clearly are in need of some education on the subject so like all good teachers, when a pupil is missing a fundamental principle on a matter,it is good teaching practice to explain that first. :)

It appears, the reason you have those views is because of what Lynn Margulis recognised.
Her rather amusing description of the study of biology, actually does recognise a fundamental problem within the environment in which biology is conducted.

Many biologists have become fixated on DNA (the genome)

For instance take the stated goal of The Human genome project ( in the projects own description)
identify all the approximately 20,000-25,000 genes in human DNA,
determine the sequences of the 3 billion chemical base pairs that make up human DNA,
store this information in databases,
improve tools for data analysis,
transfer related technologies to the private sector, and
address the ethical, legal, and social issues (ELSI) that may arise from the project.

http://www.ornl.gov/sci/techresources/H ... bout.shtml

You don't find any mention of the cell as a whole unit.
Now why is this?
After all is not the genome just a part, albeit an important one, of cellular structure?
So lets remind ourselves on what actually is the role of DNA in the context of cellular processes.?

This is a molecule that by itself is without meaning for the organism, it cannot do anything.
Harvard biologist Richard Lewontin describes it as “ a dead molecule among the most nonreactive, chemically inert molecules in the living world”.

Are all molecules involved in life processes made by DNA?
The answer is clearly NO
1) As already noted DNA by itself cannot make anything.
2) Many of the molecules that a functioning cell uses, like lipids and carbohydrates, do not come from DNA. We note that the crucial functioning of metabolism, which is the transformation of nutrients in the cell, is not in any real sense controlled by DNA. In fact metabolic processes send signals to DNA when it's services are required.
3) The proteins and non coding RNA that do derive from DNA are extensively and significantly modified by processes in the cytoplasm, in order to function correctly. In other words DNA is just a rough template of what is required.
4) Enzymes and other proteins essential for transcribing DNA are not mere products of DNA because they already have to be existing to carry out the production.
5) DNA far from being responsible for everything in the cell, is itself the responsibility of the cell to be accurately preserved

In reality all the constituents parts, including DNA originate from the cell and organism as a whole.

How is this a fact and how do we know it?

Well lets take just one strand of information, the nuclear organisation of chromosomes.

Every chromosome is positioned in a particular region or domain of the nucleus, and this territorial positioning varies with tissue type and the stage of the organism's development.
Chromosomes or parts of them near the centre of the nucleus are more intensively expressed than those near the outer periphery, which tend to be repressed. (note this is just one very simple strand of knowledge)

Now this organisational structure has nothing to do with whether a random mutation effects a particular gene or whether natural selection somehow determines this positioning. Yet this positioning correlates very specifically with the differentiating process that makes the various types of cell and tissue.
This is a level of organisation clearly above that of DNA.
Now I could go on and enumerate further on chromosome organisation but that would just be re-enforcing the point.
Also the organisation of the cell involves much more than the chromosomes themselves.

The DNA code itself undergoes a metamorphosis.
For example certain bases are subject to methylation. This is not a simple tagging or marking of these bases, but a complete transformation of the molecules that display different qualities.
Some of these methylation patterns are inherited, but for the most part they are not, and for good reason.
The undifferentiated condition of the zygote is crucial for future development. It would be disastrous if tissue specific patterns of methylation in say liver or kidney were passed on to the zygote.
Therefore in general, these patterns need to be wiped clean.
This is achieved by a wave of demethylation that is passed along each chromosome shortly after the fertilization of an egg and is completed by the time of embryonic implantation in the uterus.
Then, along comes a fresh wave of methylaion that is shaped by the embryo itself and gives a fresh epigenetic start.
If this embryonic methylation is blocked the organism dies.

So this structuring and restructuring of DNA by the surrounding processes is as central to a developing organism as the DNA code itself. However this control does not eminate from DNA.

As I have pointed out, this is but a strand of epigenetic processes that are controlled by methods beyond DNA.
Following the initial draft of the Human genome project in 2001, William Bains, chief scientific officer at Amedis Pharmaceuticals in the United Kingdom, so rightly stated
The chances that genome properties can be used to predict organismal ones is remote. Genomics and its daughter technologies are valuable instruments in the analysis of cells and tissues. They provide means of exploring biological processes and phenomena. However ... they will not often address most human needs....

The Parts List of Life,” Nature Biotechnology 19 (2001): 401-402.
So what we have here is organisation at the very highest level controlling in a top down way DNA Methylation, Differentiation and all other processes.
One overarching control of cellular processes that keeps the cell in equilibrium, but which rapidly deteriorates back down to their constituent parts at death, when this control ceases.

Now again I could go on enumerating the way in which the various processes that we have so far understood, are controlled from higher layers of organisation within the cell.

Yet, and here is the point, we have an evolutionary view, posing as scientific, that tries to project the idea that this is all explained in a bottom up method, where the whole is simply a sum of it parts and even more than that, the whole is somehow brought about by random mutations on just one of it's parts, DNA.

Is this really a scientifically credible position to take.

There is clearly nothing random about cellular life processes.
And yet to point this out so often elicits such pejorative responses. You being a good example.
It seems to me that a philosophical raw nerve is being touched.

But, just to nail down this point, study this paper about the regulation by and of p53 master sensor of stress.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857175/
Tied Up in Loops: Positive and Negative Autoregulation of p53
In part it states
Of these, p53/mdm2 is the master autoregulation loop, and it dictates the fate of an organism by controlling the expression level and activity of p53. It is therefore not surprising that this autoregulation loop is itself subject to different types of regulation, which can be divided into two subgroups...

So here we have the master controlling sensor is itself subject to a master controlling process
(one of several regulatory loops) that dictates the fate of the organism.

This master loop, is in turn regulated, in various manners, by a whole series of “multi-layered” processes, including some that are themselves “subject to direct regulation by
mdm2” — that is, they are regulated by an element of the regulatory loop they are supposed to be regulating.

It is hard to begin to describe the stunning complexity surrounding and supporting the diverse performances of the p53 protein. But it is now clear that such “regulatory” processes extend outward almost without limit, connecting in one way or another with virtually every aspect of the cell. ( And all of this is supposed to have come about by random unguided processes, Really!!)

So please when you make statements such as you have that
Complex systems are complex because they don't have one controlling influence.

(a)You are certainly not speaking from knowledge of cellular processes.
(b) Your understanding of complexity is certainly in need of further education.

Now with that little bit of education which hopefully you will have absorbed, I will be able to take you a bit further down the path of your Natural Selection ideas.
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Postby JackBean » Wed Feb 22, 2012 11:01 pm

The Human genome project is interested (only) in DNA? You must be kidding! And I though that the genome projects get usually involved in proteomics and metobolomics as well.

Again and again all the same bullshit, huh? Without DNA you will get nothing. If there are no genes, there are no lipids, no sugars, no proteins, no siRNA. Of course DNA doesn't do any real work, but guess what. That's how is it going in the cell. Nobody is arguing about that.

scottie wrote:If you look at the top left hand insert you will note it says “PubMed Central Journal List.”
How far away is that from what I wrote. Really now, is this the best you can do.?

At least on that link, before you use it as argument. http://www.ncbi.nlm.nih.gov/pmc/journals/ As you can see it is PubMed Central - Journal List i. e. list of journals listed in PubMed Central. Obviously nothing as PubMed journal.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Theories - Origin of Life

Postby wbla3335 » Thu Feb 23, 2012 12:11 am

scottie wrote:You clearly are in need of some education on the subject so like all good teachers, when a pupil is missing a fundamental principle on a matter,it is good teaching practice to explain that first. :)

You're a real hoot, scottie. The only thing a creationist can teach me is how to close my mind, which I'm reluctant to do. I haven't bothered to read very much of your last post, but what I did see didn't inspire me to waste my time on it. You might better serve yourself by being succinct and organised.
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Re: Theories - Origin of Life

Postby AstraSequi » Thu Feb 23, 2012 3:05 am

Scottie, I'd like to point out that you have not yet replied to my most recent post.
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Re: Theories - Origin of Life

Postby canalon » Thu Feb 23, 2012 4:58 am

scottie wrote:You could argue but I take it you are not going to then. :)
If you look at the top left hand insert you will note it says “PubMed Central Journal List.”
How far away is that from what I wrote. Really now, is this the best you can do.?


In fact I should apologizing for posting by error only the beginning of an answer to take care of my mini monster at home, and never corrected or completed as I did not have time to come and correct my mistake. So yes, Scottie I will not argue your lack of attention to details.
What I wanted to say is that your wondrous paper written by the now provably mentally troubled Dr Abel (see astrasequi post), and the competent but Weird Jack Trevors in Theoretical Biology & Medical Modelling, although published does not have garnered a strong interest: If you look on google scholar you will notice that it has been only cited by its own authors. Usually not a good sign. As a biologist, and not an information scientist, it is hard to comment on the content. Neither has the notion of functional sequence complexity, which seems to have originated in this paper, seem to have caught on much beyond Dr Abel's own paper.

But if I understand what is explained Abel and Trevors are arguing that in order to create a self replicating molecule, it would somehow require that a molecule was able to constrain the sequence that will follow (i.e If A then B then C then D, etc...) in order to be able too create enough copy of itself. That would be interesting, but AFAIK that is not what evolution argue. Which would be closer than a molecule that made it just a bit more likely to increase the formation of identical molecules in solution was our very first ancestor. In fact that the monomers do not need to carry any information, just that a finished product can constrain the world around it. And since that would make the notion of FSC irrelevant, that would explain why the absence of disproving the 4 null hypothesis as little to no interest.

But before you answer this post will you answer my question about the circularity of the designer argument? Or even Astrasequi's question.

By the way, I am tired of your refusal to answer direct questions simply and your refusal to enter a discussion. So will you finally answer? Preferably in less than your usual 140 + k signs
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Postby LeoPol » Thu Feb 23, 2012 11:45 am

(richarddawkins.net/articles/643549-origin-of-life-challenge-how-did-life-begin#page4) :P

In order for a origin of membrane - much organic matter is not necessary - only the membrane lipids of different isoforms, it is necessary also to a weak emission core of the star created a flow of heat through the surface phase transition, and yet not interfere with a certain oscillation - vibration … In general, all this is difficult to discuss now, not yet studied the process of emergence and functioning in a natural cell membrane of this very … - Active situational model - a kind of natural intelligence and personality!! But when it all becomes clear, then we can speculate about the conditions and awakening him to the protostar, or on some planet out there.

So. Life has two interacting components. One component - natural intelligence. The second component - the polypeptide-nucleic technology - a self-contained database on DNA, which is implemented through the input-output - RNA into the polypeptide interface. What comes first? I believe that natural intelligence is primary, and polypeptide-nucleic technology - is secondary. In this sense, the theory of “Evolution of the primary replicators to Homo Sapiens” should be replaced by a theory of “Abiogenesis, and social development of the primary natural intelligence”, which later created and developed polypeptide-nucleic technology. http://richarddawkins.net/articles/6435 ... egin#page4
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Re: Theories - Origin of Life

Postby Nick7 » Fri Feb 24, 2012 1:31 am

wbla3335 wrote:
Nick7 wrote:Therefore, allocating the role of the designer to “the natural world” also seems to be quite subjective to me, and I don’t see how one can rationally quantify it (likely or unlikely…)

Everything that goes on in heads is subjective, but some of it can be based on evidence. In the absence of evidence for the supernatural, some of us consider the natural to be more likely. Some of us don't. .

Well, 1st, it depends on what you choose to use as a starting point to measure your “natural”. (sorry for the delay, by the way). Life is a sophisticated carbon-based nanotechnology and it heavily relies on preconditions. Where did the preconditions for the complex life come from? AstraSequi , on the previous page, used dice in the example ( “If you roll a pair of dice, your chance of a double 6 is quite low (1/36). However, if you try… a hundred times times, ...it would be more surprising if you didn't get it at least once.” ) What if I give you a pair of dice with no 6 present on them at all, how many tries do you need to roll a double 6? I’ve tried to make this point several times… Why do you assume that preconditions just happened? For instance, what known cosmic law states that every universe popping into existence must have so many constants in physics? What known cosmic law requires nuclear resonances in the creation of fundamental blocks of life (Carbon and Oxygen, in our case) to be so “tuned”? ......the point is that you choose to assume that all the fundamental pillars of our existence just happened through some unknown, but purely mechanistic and unguided processes. Now, I can’t find my membership card of the The National Academy of Sciences and my pooch has chewed the certificate confirming my Ph.D. in Molecular Genetics, but I’ll risk to state that I see one fat-%#s axiom sitting in the foundation of your reasoning that leads you to that concept of “unlikely” behind the idea of “creation”. Evolution doesn’t really seem to falsify creation, it falsifies the meaning you put into the word creation (the way you believe it should’ve happened if it were true).

wbla3335 wrote:
Nick7 wrote:And he usually provides links to the opinions of the more-than-qualified individuals.

He provides links to studies. The opinions he gives are his own. The authors of the studies are not claiming the falsification of evolution nor the existence of a designer.


Here is the original opinion on F. Collins' Brown Rat one by Sternberg I mentioned before http://www.evolutionnews.org/2010/03/be ... 32981.html (maybe it's just a reprint on ID site, but that's where the Scottie's opinion in this case came from). I’ve really got no time to google them all up, but I’d say that I think that at least 50% (and it’s very conservative estimate) of the opinions presented by Scottie were most likely originated by the peers of the papers' authors. But those are opinions. End if studies' authors have atheistic opinions attached to the findings of their research, those are also just opinions. That’s where I differ from both you and Scottie… ALL of us are not talking science here. We’re talking philosophy encrusted with supporting scientific evidence. Speaking of which….
It’s not that there is no evidence of what you call “supernatural” (don’t really like this word). It’s what you would or wouldn’t accept as evidence. Scientific method works well with the evidence which supports purely mechanistic and consistently replicable natural phenomena. For instance, nobody questions the validity of the quantum entanglement in physics, even though this bizarre phenomenon is absolutely not understood and appears to be rooted somewhere beyond the realm of observable reality. Why? Because it’s easily replicable in any properly equipped lab in the world. Once you move into grey areas, scientific method can (and does) sometimes falter under the weight of biases, preconceptions, dominant believes, politics, etc. Here is an interesting article on that http://www.newyorker.com/reporting/2010 ... ntPage=all ). The article describes the “decline effect”… A couple of extracts: “...selective reporting is everywhere in science….We cannot escape the troubling conclusion that some—perhaps many—cherished generalities are at best exaggerated in their biological significance and at worst a collective illusion nurtured by strong a-priori beliefs often repeated.” ….. Such anomalies demonstrate the slipperiness of empiricism. …. We like to pretend that our experiments define the truth for us. But that’s often not the case. Just because an idea is true doesn’t mean it can be proved. And just because an idea can be proved doesn’t mean it’s true. When the experiments are done, we still have to choose what to believe."
So....for example, would you accept a possibility of “supernatural” explanation for this http://www.sheldrake.org/Articles&Paper ... e_abs.html ? Why not? If there is something else out there as far as general relativity and quantum physics go, why our (and animal) consciousness is being ordered to stay within our skulls if the experiments above (and collective experiences of numerous people) suggest other possibilities? Has our consciousness been already dissected and reduced to the molecules in our brains?

And one more thing........ about collective experiences. I like science, but I don’t like scientism. Yes, everything that goes on in heads is subjective (as you’ve put it), but it’s still an experience. If these collective experiences make similar independent claims (across different ages, continents and cultures), it makes me suspicious that there might be something behind them. When Dawkins was asked about it, he said that his personal “anecdotal experiences” © do not matter. Well, not everyone is as lucky as Dawkins.
To make a long story short… I view the position outlined by neuroscientist D. Eagleman ( http://en.wikipedia.org/wiki/Possibilianism )as being more scientifically honest: "Our ignorance of the cosmos is too vast to commit to atheism, and yet we know too much to commit to a particular religion. A third position, agnosticism, is often an uninteresting stance in which a person simply questions whether his traditional religious story (say, a man with a beard on a cloud) is true or not true. But with Possibilianism I'm hoping to define a new position -- one that emphasizes the exploration of new, unconsidered possibilities. Possibilianism is comfortable holding multiple ideas in mind; it is not interested in committing to any particular story."
wbla3335 wrote:Your beliefs, scottie, are shared by very few people in this world, and you may want to ask yourself why that is. There are lots of theists, fewer deists…

This one is easy. To become a deist or an atheist or …. whoever other non-certifiably-theist, one has to start thinking. Thinking, just like anything else, requires prerequisites – extra time, education, etc. And most of the people just do not have that kind of luxury. Most of the people in this world are born into their believes, and after that they literally survive on several bucks a day; therefore, they do not think about the origins of their existence, but they mostly think about how to maintain their existence and how not to pop out of it prematurely. And why would anyone be deterred from independent thinking by the “majority” argument anyway? Even in science there is an expression “Science advances one funeral at a time”. And outside of science, following the majority is one of the most assured way to fall off the cliff.

wbla3335 wrote:Complex systems are complex because they don't have one controlling influence.

Actually, I also stumbled over this one. Complex systems are indeed complex because they have a gadzillion number of variables defining them. We owe to this complexity, without it no complex creatures would exist (that’s how I started this post). But outside of our bodies, complex interactions result in what is studied by the chaos theory. If I try to predict a precise trajectory of a little slice of, ….. lets say, polyurethane foam sucked into my vacuum cleaner, I doubt that it can be easily done. But based on the “controlling influence” of the vacuum cleaner properties and, most importantly, the “controlling influence” of the structure of polyurethane, I can predict that not only my slice of foam will stay intact, but it will also “adapt” its shape to the shape of the trash it’s squeezed against inside, whatever that may end up to be. You take that embedded “plasticity” that took us from a cosmic dot to Precambrian slime to A. Einstein for granted, and I have to be convinced.
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Re: Theories - Origin of Life

Postby canalon » Fri Feb 24, 2012 2:55 am

Nick7 wrote:Why do you assume that preconditions just happened? For instance, what known cosmic law states that every universe popping into existence must have so many constants in physics? What known cosmic law requires nuclear resonances in the creation of fundamental blocks of life (Carbon and Oxygen, in our case) to be so “tuned”? ......the point is that you choose to assume that all the fundamental pillars of our existence just happened through some unknown, but purely mechanistic and unguided processes. Now, I can’t find my membership card of the The National Academy of Sciences and my pooch has chewed the certificate confirming my Ph.D. in Molecular Genetics, but I’ll risk to state that I see one fat-%#s axiom sitting in the foundation of your reasoning that leads you to that concept of “unlikely” behind the idea of “creation”. Evolution doesn’t really seem to falsify creation, it falsifies the meaning you put into the word creation (the way you believe it should’ve happened if it were true).


You are very right and very wrong at the same time. You are right that no law or anything else requires anything from any universe popping in existence. And that the fact that all the atoms are tuned so wonderfully (whatever that means) is essential to our existence. But you are very wrong in that it is not because of us that those things are so well tuned to allow life, but that life as we know it is there only because all those stuff happened to work together. If they had not been, you would not be there mistaking causes for consequences. For all we know there might be an infinite number of universe devoid of stupid creatures to wonder how nice was their non existent creator to tune everything to allow them to exist...
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Re: Theories - Origin of Life

Postby AstraSequi » Fri Feb 24, 2012 4:57 am

Life is a sophisticated carbon-based nanotechnology and it heavily relies on preconditions. Where did the preconditions for the complex life come from? AstraSequi , on the previous page, used dice in the example ( “If you roll a pair of dice, your chance of a double 6 is quite low (1/36). However, if you try… a hundred times times, ...it would be more surprising if you didn't get it at least once.” ) What if I give you a pair of dice with no 6 present on them at all, how many tries do you need to roll a double 6? I’ve tried to make this point several times…

...I'm quite sure I was talking about something completely different, specifically mutations. The analogy is meant to show that if there is a small chance of something, then you can be very certain of getting lucky if you try enough times. You can replace the analogy with two one-million-sided dice if you want, so long as you get a trillion chances.

If you want to claim that there is literally zero chance for something to happen, you need a rigorous mathematical proof - nothing else is sufficient.


Also, a few other points that I thought I should mention (I suppose I'm jumping into someone else's discussion, but I like talking about science at the philosophical level :)):

Why do you assume that preconditions just happened? For instance, what known cosmic law states that every universe popping into existence must have so many constants in physics? What known cosmic law requires nuclear resonances in the creation of fundamental blocks of life (Carbon and Oxygen, in our case) to be so “tuned”? ......the point is that you choose to assume that all the fundamental pillars of our existence just happened through some unknown, but purely mechanistic and unguided processes.

It is not an assumption - it's just that there is no evidence in any direction (at least as far as I know). For example, there is no way to falsify the hypothesis that our universe was created by highly advanced aliens, and I probably wouldn't be surprised if this were true. However, since pretty much everything else in physics is "mechanistic and unguided," it is reasonable to say that this might be as well.

Also, if you wish to make a fine-tuning argument, you must remember to consider the anthropic principle. (See http://www.anthropic-principle.com/primer.html, and also canalon's previous post.)

Evolution doesn’t really seem to falsify creation, it falsifies the meaning you put into the word creation (the way you believe it should’ve happened if it were true).

I don't think this makes sense. The only thing that you can falsify is a hypothesis.

Scientific method works well with the evidence which supports purely mechanistic and consistently replicable natural phenomena.

The scientific method works well with consistently replicable phenomena. As long as causality exists and remains consistent, the scientific method will work.

So....for example, would you accept a possibility of “supernatural” explanation for this http://www.sheldrake.org/Articles&Paper ... e_abs.html ? Why not?

The probability of bias or error in a single study is much higher than the probability that a "supernatural" force exists, times the probability that this force enables telepathy over long distances, times the probability that it is occuring in this circumstance, times the probability that nobody else would have found rigorous evidence for it even though it actually existed...This is where you get the phrase, "extraordinary claims require extraordinary evidence."

That being said, a possibility? Sure - the only impossibilities are those that have mathematical proofs behind them. However, the probability is so low, given our current state of knowledge about how the universe works, that it is not reasonable to think that it might be true.

Also, perhaps on an unrelated note - the definition of "supernatural" is basically equivalent to "that which cannot be explained by science," so I would call it a truism that science only explains things that are "natural." If science explains something, then it is no longer considered supernatural (for example - sunrise, reproduction, rainbows.) So I would say that I don't like using the word "supernatural" either. :)
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Re: Theories - Origin of Life

Postby wbla3335 » Fri Feb 24, 2012 5:57 am

Thanks guys, you've saved me a lot of bother. For me, "supernatural" simply means outside of nature.
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Re: Theories - Origin of Life

Postby AstraSequi » Fri Feb 24, 2012 6:25 am

You're welcome, then. :) (Still, though, I didn't respond to everything, if there's anything else you want to reply to.)

wbla3335 wrote:For me, "supernatural" simply means outside of nature.

I agree with this as well - I would just say that "nature" is the same thing as "everything that can (in principle) be explained by science." I can't really think of anything that might be in principle unexplainable by science - or perhaps a better way to say it would be, something that is impossible in principle to gather evidence about, under any circumstances of time, space, etc - yet not be considered "supernatural."

Of course, part of the point was that the word doesn't have a very useful meaning, so I suppose it doesn't matter. :)
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Re: Theories - Origin of Life

Postby scottie » Mon Feb 27, 2012 10:59 am

AstraSequi

I have just returned to the forum after being away for a few days.
Which question of yours do you wish me to address?

Also
Canalon could you repeat your question please.

Thanks
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