Kevin's Watch

Thanks. Although I can't "picture" it, the concept is fairly clear, particularly because I'm a keen snooker player.

The less "free space," (or the more constrained the space), the greater chance of collision. And if it's happening millions of times with millions of "units" the chance is proportinately greater.

--A

Except that the "primordial soup" was not made simply of nucleotides... there was all sort of stuff in there. To continue the analogy with biliard balls, you have to imagine that:

1) the biliard balls are moving in three dimensions in a place filled with golf balls, basketballs, marbles, tennis balls, and so on;

2) Given these conditions, you need to reach an end result of at least about 50 biliard balls placed in a certain sequence and not just touching the previous and next one, but actually being bound to it.

As for:

Prebe wrote: have heard, however, that the assembly of prebiotic RNA molecules might have been hugely faciliated by clay-like minerals that had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules (nucleotides or building blocks to the non-biologist). Such a template would provide an environment for "experimentation" many orders of magnitude more "fertile" than a puddle. (I'm starting to write like "The" Esmer )

I never heard of this, but even if it were true, then the next question would be "how coincidental is it that those clay-like minerals had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules"?

You know what's annoying? I don't know where Xar lives, but it's obviously closer to Prebe's & Av's time zones than to mine. So nobody says anything all day. Then I get up in the morning, and WHAM!!! rassin' frassin'...

Avatar wrote:What we're really looking for is some starting point I guess, to see whether there really is support for the idea of ID. We are though, I think, sorely hampered by the lack of, say, an RNA fossil record...there isn't any way for us to tell how many variations and layers of complexity were added from that base point.

This sums up the thread, and my initial post, perfectly.

Xar wrote:If you want an idea of how complex is the biochemistry of a single cell, you might want to glance at these pictures (they are electronic versions of wallpapers a scientific company used to print a few years back, so they're even outdated as we know more now!):

www.expasy.ch/cgi-bin/show_thumbnails.pl

www.expasy.ch/cgi-bin/show_thumbnails.pl?2

Unbelievable!!! A magazine once printed the first four seconds of some U2 song's binary code. It took two pages of extremely small print to fit all the 1's and 0's. I thought that was impressive, but not compared to this! It's easy to see why people can't accept that such a thing was not planned, but I resist the urge to join them. I believe such a thing could develop from something much simpler.

Let's see... Av's next post is perfectly stated.

Xar wrote:Well, the problem is that as far as we know, considering our knowledge, there is nothing that could have predated RNA and still be considered "life". RNA is a complex molecule, although it is simpler than DNA, and if you want to start chemical processes through catalysis, replication and so on, you absolutely NEED this sort of complexity. No other known common molecule can replicate itself and simultaneously allow for an increase in its own complexity, and if you look at chemical properties, it turns out that, quite simply, there could be no other molecule which could take on the same role as RNA did.

So why must we consider anything that could have predated RNA "life"? On Star Trek:TNG, Dr. Crusher said this during a conversation with Data: "Well, the broadest scientific definition might be that life is what enables plants and animals to consume food, derive energy from it, grow, adapt themselves to their surrounding, and reproduce." But if some molecule can do nothing more than (Ha!) replicate itself, but the method used cannot prevent changes from occurring now and again, it could eventually lead to life. But you, Xar, said earlier (I think?) that this is what RNA is considered by many to have done. So the question is: Can such a molecule have formed by nothing more than its component parts bumping into each other?

(I think I just restated a lot of stuff, but I want to make sure I'm on the same page as you guys.)

Xar wrote:Have you ever wondered why we are carbon-based life forms? Because carbon is the only element (out of more than 100) that, binding with other carbon atoms, can form long chains of atoms (which are absolutely essential, say, for lipids, which form the cell's membrane - but also for RNA and DNA, which are based on ribose and deossiribose, which in turn are carbon-based as well). Silica is the only other element capable of doing something like that, and even then it cannot support longer chains than 6-7 atoms, as I recall.

I suggest you NOT say this to a Horta!

Xar wrote:So the question that remains, which is unanswered even as of now, is - how did all those free-floating bases aggregate to form a RNA strand long enough to be able to bend and made just so that it could catalyze its own reproduction?

OK, here it is again.

Xar wrote:Due to chemical bonds and properties, a protein, or a DNA strand, or a RNA strand can't bend any conceivable ways: there are only some ways in which it can bend, the rest of them being impossible due to "encumbrance". Experiments done decades ago did show that, re-creating the conditions that geology tells us Earth experienced when life emerged, we can produce the "building blocks" of RNA and DNA - but such experiments did not show any binding. Of course, one could always argue that, given enough time and amount of materials, you would inevitably get at least one such molecule - but this argument sounds suspiciously like the classical argument that you will undoubtly get all of Shakespeare's works if you put an infinite number of monkeys in front of an infinite number of typewriters and let them type for an infinite amount of time.

I don't believe for a second that the monkeys would ever produce Shakespeare's works. I think it's just as likely (that is, not at all likely) that every monkey would hit nothing but the E key forever. There's an infinite number of strings of gibberish that could be typed, which I think is more likely than Shakespeare. Or tons of gibberish with lots of words thrown in on occasion. But I do not believe we would ever find: To be, or not to be? That is the question. Whether 'tis nobler in the mind to suffer the slings and arrow of outrageous fortune, or to take arms against a sea of troubles, and, by opposing, end them. And on and on for hundreds of pages.

Xar wrote:As for the "fragility" of life, Avatar... ironically, life becomes more fragile the more "complex" the organism is - mostly because the number of biochemical processes increase, and communication among the various cells that make up a multicellular organism is vital.

Same with cars, eh? The Model-T was probably something I could have maintained and fixed. These days, fuggedaboudit.

Xar wrote:But if you take bacteria, for example, there are many of them who can live up to 130°C comfortably, and others which, if food is scarce or the temperature changes so they can't live anymore, just turn themselves into spores and sit there, waiting, even years if need be, until the conditions change back and they can return to life. To give you an example of how difficult is to remove life, did you know that NASA once ran an experiment in which they took bacteria in space, exposing them to the vacuum and cold of space, and when they returned on Earth, they were still viable? And that these results prove that bacterial life at least could survive a short trip into space? There are bacteria who can survive being bathed in radiations!

For that matter, many insects could likely survive a nuclear holocaust...

I heard that a tick can live in a jar of sand for two years.

Xar wrote:Of course, we couldn't, but that's because we are extremely fine-tuned, and if even just one of our "life-support" systems fails, we're in trouble - but life itself is much more resilient than it is commonly thought. In fact, someone once said that once life has appeared, you can never truly destroy it - it always survives somehow.

Jeff Goldblum in Jurassic Park. heh

Xar wrote:2) Given these conditions, you need to reach an end result of at least about 50 billiard balls placed in a certain sequence and not just touching the previous and next one, but actually being bound to it.

Could they have met, one at a time? I mean, would they have bound to each other, then remained bound until the next came along, then the next, etc, until the molecule was complete? Otherwise, the 50 would have had to have met all at the same time, in the proper positions.

Xar wrote:

Prebe wrote:I have heard, however, that the assembly of prebiotic RNA molecules might have been hugely faciliated by clay-like minerals that had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules (nucleotides or building blocks to the non-biologist). Such a template would provide an environment for "experimentation" many orders of magnitude more "fertile" than a puddle. (I'm starting to write like "The" Esmer )

The keyword being: Facilitated steric interactions: Simple minerals being catalysts (scafolds) of experimentation in complexity.

I never heard of this, but even if it were true, then the next question would be "how coincidental is it that those clay-like minerals had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules"?

I'm kinda sceptical about this, also. Assuming, of course, I understand what Prebe is saying. But it sounds like we've lost the need for a molecule's origin, and now have that molecule's mold's origin to figure out.

Fist and Faith wrote:

Xar wrote:Well, the problem is that as far as we know, considering our knowledge, there is nothing that could have predated RNA and still be considered "life". RNA is a complex molecule, although it is simpler than DNA, and if you want to start chemical processes through catalysis, replication and so on, you absolutely NEED this sort of complexity. No other known common molecule can replicate itself and simultaneously allow for an increase in its own complexity, and if you look at chemical properties, it turns out that, quite simply, there could be no other molecule which could take on the same role as RNA did.

So why must we consider anything that could have predated RNA "life"? On Star Trek:TNG, Dr. Crusher said this during a conversation with Data: "Well, the broadest scientific definition might be that life is what enables plants and animals to consume food, derive energy from it, grow, adapt themselves to their surrounding, and reproduce." But if some molecule can do nothing more than (Ha!) replicate itself, but the method used cannot prevent changes from occurring now and again, it could eventually lead to life. But you, Xar, said earlier (I think?) that this is what RNA is considered by many to have done. So the question is: Can such a molecule have formed by nothing more than its component parts bumping into each other?

Well, I think this question is also tackled later

Fist and Faith wrote:

Xar wrote:2) Given these conditions, you need to reach an end result of at least about 50 billiard balls placed in a certain sequence and not just touching the previous and next one, but actually being bound to it.

Could they have met, one at a time? I mean, would they have bound to each other, then remained bound until the next came along, then the next, etc, until the molecule was complete? Otherwise, the 50 would have had to have met all at the same time, in the proper positions.

Well, of course they could have remained bound to each other until the next one came along - except for the fact that they'd still be bumped around by basketballs, tennis balls, golf balls, marbles, and who knows what else - all the while, a huge propane torch is placed directly above them. That more or less would mirror the few nucleotides aggregating together while all sorts of molecules bump into them (and conceivably could steal nucleotides as well, or attach themselves and terminate the molecule) and the sun is throwing a lot of radiations into the boiling cauldron...

Fist and Faith wrote:

Xar wrote:

Prebe wrote:I have heard, however, that the assembly of prebiotic RNA molecules might have been hugely faciliated by clay-like minerals that had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules (nucleotides or building blocks to the non-biologist). Such a template would provide an environment for "experimentation" many orders of magnitude more "fertile" than a puddle. (I'm starting to write like "The" Esmer )

The keyword being: Facilitated steric interactions: Simple minerals being catalysts (scafolds) of experimentation in complexity.

I never heard of this, but even if it were true, then the next question would be "how coincidental is it that those clay-like minerals had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules"?

I'm kinda sceptical about this, also. Assuming, of course, I understand what Prebe is saying. But it sounds like we've lost the need for a molecule's origin, and now have that molecule's mold's origin to figure out.

[/quote]

That's the same idea I have about the argument astronomers have as to whether life originated on Earth or not... some say it came on a meteor, but then at that point all you are doing is moving the question from "how did life originate?" to "how did life originate in some place we ignore and then travel to Earth?". You will notice that both sets of questions relate to life; usually I tend to believe that this is just an attempt to distance yourself from the unavoidable question "so, where does life ultimately come from?"

Xar wrote:

Fist and Faith wrote:

Xar wrote:2) Given these conditions, you need to reach an end result of at least about 50 billiard balls placed in a certain sequence and not just touching the previous and next one, but actually being bound to it.

Could they have met, one at a time? I mean, would they have bound to each other, then remained bound until the next came along, then the next, etc, until the molecule was complete? Otherwise, the 50 would have had to have met all at the same time, in the proper positions.

Well, of course they could have remained bound to each other until the next one came along - except for the fact that they'd still be bumped around by basketballs, tennis balls, golf balls, marbles, and who knows what else - all the while, a huge propane torch is placed directly above them. That more or less would mirror the few nucleotides aggregating together while all sorts of molecules bump into them (and conceivably could steal nucleotides as well, or attach themselves and terminate the molecule) and the sun is throwing a lot of radiations into the boiling cauldron...

Well, that certainly sounds problematic. But what I meant is, do those atoms normally bond individually? I don't have the slightest idea what atoms we're talking about, but will an X atom and Y atom normally bond under ever perfect circumstances? And then a Z atom comes along and bonds to one end or the other? Then another X, or an A, or whatever? Or do these atoms only bond to their neighbors in the RNA chain if the entire chain is assembled? I don't know if I'm making sense... I know what I mean, but... Do fragments of RNA exist, just hanging out, doing not much of anything, free to join with other fragments of RNA?

Plenty of evidence to support the mineral theory Xar:

www.biolbull.org/cgi/reprint/196/3/311.pdf
(General on polymerisation and the mineral catalysis theory)

www.georgealozano.com/teach/evolution/p ... no1996.pdf
(slightly sceptical of the RNA world view, but interesting special has some food for thought on the significance of rate constants (build-up/brake-down) of organic polymers, for the evolution of information systems.

sciencemag.org/cgi/content/abstract/302/5645/618
(something about formation of membranes as well)

www.ncbi.nlm.nih.gov/entrez/query.fcgi? ... t=Citation

www.iupac.org/publications/pac/2004/pdf/7612x2085.pdf
(A good review. If nothing else, read page 2088 (not recommended for non-scientists )

For more info, try searching for - clay mineral RNA polymerization – on google.scholar

As for the RNA world, it looks like many scientists think, that it was not RNA per se, but some polymer that resembled it.

About the carbon based thing, remember the peptide bond (C to N) and the bonds in RNA and DNA (Phosphor-ester bonds). Speaking of which, poly phosphate can grow to quite extreme lengths without any carbon involved.

As for the Creation thing (Xar) am I correct in assuming, that the more we explain, the further back you would move the point of divine influence? If this is so, would you actively try to push this border yourself without fear of loosing faith? Any scientist should be able to answer yes to that question.

My advice is to both Fist and Xar is: don’t pin any faith on science, you might end up frustrated when you have to push the barrier further and further back. This is mainly a problem for people like you, who actually understand what the scientists are saying. Many other believers can just hang on to their faith.

A brief look at those links tells me they're more for Xar than for me, but I'll see what I can make of them. They're certainly along the lines of what I'm asking about.

Prebe wrote:My advice is to both Fist and Xar is: don’t pin any faith on science, you might end up frustrated when you have to push the barrier further and further back. This is mainly a problem for people like you, who actually understand what the scientists are saying. Many other believers can just hang on to their faith.

I don't usually understand what the scientists are saying! But for me, the nature of the possible answer is important. The information I'm getting here may be keeping me more firmly on the fence, but, then, I'm not understanding all the information yet. I really hope to learn more about these clay-like minerals you mentioned!

The problem now is, that we are dangerously close to the point where my understanding of the sci-lit is becomming flimsy. I have only an intermediate level understanding of chemistry, and chemistry is where we are going, if we continue.

Many of the links I posted contain detailed chemical descriptions of reactions, and I honestly don't understand all the details (at least not without a lot of looking up and intense study, that I am not going to put in). However, I have so much faith (yes, I said it) in my fellow scientists, that I believe in the conclusions a chemist, an astronomer or a physicist draws from their research.

There is a limit to what everyone can understand. My question is: should we all, when we hit our separate limit, start believing, or should we take someones word for it? Someone who are likely to know a lot more about it than we do ourselves?

And this, I believe, is really the crux (again pardon the expression) of the discussion: Do you trust the scientists at their word, assuming that they constantly do all within their power to prove or disprove their hypotheses using the latest scientific tools? (knowing that they may be wrong, but have at least ACTIVELY looked for an answer)

Or do you believe, that we have found out all that is to know using present scientific methods, and any explanation before that can be conveniently ascribed to a higher power?

What I am saying is: The point where you don't personally understand anymore, is not necessarily the point where you should start believing. But the moment you start believing could be the moment you stop looking for answers.

I am NOT saying this to put people off believing. I am saying this to prevent people from contending themselves with the scientific status quo.

I'm in GMT +1 by the way

Prebe wrote:The problem now is, that we are dangerously close to the point where my understanding of the sci-lit is becomming flimsy. I have only an intermediate level understanding of chemistry, and chemistry is where we are going, if we continue.

Just to show you how little I know about all this, I thought we were talking chemistry pretty much this whole time!

Prebe wrote:Many of the links I posted contain detailed chemical descriptions of reactions, and I honestly don't understand all the details (at least not without a lot of looking up and intense study, that I am not going to put in). However, I have so much faith (yes, I said it) in my fellow scientists, that I believe in the conclusions a chemist, an astronomer or a physicist draws from their research.

I have often defended science to other Watchers, because, despite my lack of understanding most of it, the fruits of its labors are obvious. Theories are presented. The more times the theory is tested and NOT proven wrong, particularly if the tests are of diverse natures, the more faith I have in the theory. In addition, some theories, or at the very least, aspects of them, seem to be proven correct. Hawking says that navigational satellites don't give accurate information until we take the different rates of time, due to Einstein's relativity, into account.

Prebe wrote:There is a limit to what everyone can understand. My question is: should we all, when we hit our separate limit, start believing, or should we take someones word for it? Someone who are likely to know a lot more about it than we do ourselves?

And this, I believe, is really the crux (again pardon the expression) of the discussion: Do you trust the scientists at their word, assuming that they constantly do all within their power to prove or disprove their hypotheses using the latest scientific tools? (knowing that they may be wrong, but have at least ACTIVELY looked for an answer)

This is exactly what I'm after. What IS the scientists' word? I can't tell from all of this. RNA was the beginning, and there's no clear guess on how it formed? Are the "molds" you mentioned the most commonly believed theory of how RNA came about? Do molds like this exist now? Do they know how such molds came about? Something else entirely? (Nor can I tell if they are saying, "This is the way it happened," or, "Based on what we can observe happening now, it's certainly possible for this to have happened then.". The first attitude I laugh at, while I appreciate the second. But I consider the information presented in either case. And I know that the information may be entirely reconsidered at some point, as I gather is now the case with the thought that the first life form was protein based.)

Which brings up the question that I'm not sure has been answered yet. (Of course, it may have been, even if I didn't recognize it as such.) What was observed that proved the protein-life-form theory to be wrong? Why was it discarded for the RNA theory? (LOL Until this thread, I thought RNA and DNA were some sort of protein molecules.) Are there ways I'm not aware of that have yet to be mentioned to test whether any of these ideas actually are the answer? Or are we only able to test and observe to see if something couldn't have happened? (Not that "only able to test" is not a significant thing. I imagine every theory that gets ruled out strengthens the remaining theories.)

I know I'm asking quite a bit. I don't expect all of my questions to even have answers, and I am certainly not trying to put pressure on you, or anyone else, to answer them. But I don't think my questions are unreasonable. In fact, I think they are the types of questions that lead to solid, scientific research.

Prebe wrote:Or do you believe, that we have found out all that is to know using present scientific methods, and any explanation before that can be conveniently ascribed to a higher power?

Not being able to scientifically explain beyond a certain point does not prove a higher power's existence. However, not being able to scientifically explain beyond that point certainly doesn't prove there is a scientific explanation.

Prebe wrote:What I am saying is: The point where you don't personally understand anymore, is not necessarily the point where you should start believing. But the moment you start believing could be the moment you stop looking for answers.

The last sentence is certainly the danger I see. Which is, of course, why I started this thread. The point where I don't personally understand anymore was passed long ago. I knew my thought that it might proof of a designer's existence was based on ignorance, so asked others (particularly you and Xar) for more information.

Prebe wrote:I'm in GMT +1 by the way

Yeah, I know you're in Denmark, and Av's in SA. But Xar's location field, like mine, isn't quite as specific as that. One could easily ask where in the Westron Mountains I am. It's a pretty big piece of real estate, after all.

:::I am so lost:::

:::sigh:::

I really did try keeping up with you guys...

Xar wrote:

Prebe wrote: have heard, however, that the assembly of prebiotic RNA molecules might have been hugely faciliated by clay-like minerals that had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules (nucleotides or building blocks to the non-biologist). Such a template would provide an environment for "experimentation" many orders of magnitude more "fertile" than a puddle.

I never heard of this, but even if it were true, then the next question would be "how coincidental is it that those clay-like minerals had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules"?

Think you're looking at it the wrong way round...I'm thinking more along the lines of "Because of that particular structure, the units had an opportunity to match."

And hey, if there is no creator, then coincidence not only must have played, but must continue to play a role of some sort. Coincidence is a real phenomenon, random chance causing an apparently unlikely event by bringing two or more existing things together. It happens, and while it's all very well to distrust them, (especially in terms of motives), that in no way detracts from their occurrence.

You meet a man in a bar, talk to him, turns out...his number is one digit different from yours...or his son goes to the same school as your son...or his mother was your fathers ex-wife...whatever. It happens, and either its a coincidence, or some power is consciously directing every event in your life. Which is more likely?

I just don't think that we can so confidentlly dismiss the possibility of coincidence. Even taking your vastly busy 3-d space with the flying balls of all sizes, (which makes perfect sense, I'll certainly agree), even without Prebe's little grooves to help things along, with hundreds/millions/billions? of those base components flying around, some will be jostled by the bigger objects, some will be shielded by them, in some spot, with just the correct circumstances, by pure chance, (like a single seed falling on the only crack in the concrete, getting just the right amount of light and moisture to germinate), some bound and flexed in just the right way.

What's the chance of any given asteroid or comet in the vastness of the universe intersecting with earth? Infintesimal. How many times has earth been struck by asteroids/comets? Quite a few.

(Oh yeah, I'm GMT +2, I think Zar is somewhere in Europe, (Germany? Italy? ) and Fisty is about GMT -5 or -7 I guess. )

--A

Avatar wrote:

Xar wrote:

Prebe wrote: have heard, however, that the assembly of prebiotic RNA molecules might have been hugely faciliated by clay-like minerals that had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules (nucleotides or building blocks to the non-biologist). Such a template would provide an environment for "experimentation" many orders of magnitude more "fertile" than a puddle.

I never heard of this, but even if it were true, then the next question would be "how coincidental is it that those clay-like minerals had molecular grooves with a spacing that was a pretty exact match between units in RNA molecules"?

Think you're looking at it the wrong way round...I'm thinking more along the lines of "Because of that particular structure, the units had an opportunity to match."

I wish I knew anything about this clay-like stuff. I really don't know how to envision this. Prebe, I assume these kinds of things are still around? And there are lots of different patterns of grooves, one of which is the RNA match in question?

Or are you saying that there was only one template, and any atoms could have fit into these grooves (and who could imagine how many did), but only RNA's specific molecules in their specific order benefitted by it?

Or are you saying something else that, due to being in way over my head, I can't envision?


And I'm GMT-5.

I wish I knew anything about this clay-like stuff. I really don't know how to envision this. Prebe, I assume these kinds of things are still around?

Yes they are. Quite common. They were used to perform some of the polymerisation experiments in the links I posted. Think lego blocks thrown at random into a box and hope the stick together. They will need to meet, and they will need to be in the correct orientation in three dimensions.

Then think the same blocks placed in betwen two rulers on a table. These WILL meet, because they move (molecules do that above 0 K). Now the only thing needed for the blocks to stick is the correct orientation. Not in three but two dimensions. Xar throws a perfectly logical onion in that ointment by saying, that there was several other building blocks present that migth have muddied the picture. That is absolutely true. However, the great variation in three dimensional structure of crystal latices in different minerals would mean, that somewhere out there, there would have been a mineral with "grooves" that preferentially (if not exclusively) accomodated RNA subunits.

And there are lots of different patterns of grooves, one of which is the RNA match in question?

Something like that yes.

Or are you saying that there was only one template, and any atoms could have fit into these grooves (and who could imagine how many did), but only RNA's specific molecules in their specific order benefitted by it?

In 1000 minerals there must be a 1000+ different patterns of molecular grooves. One or more such minerals probably fitted RNA subunits (not the atoms, but the nucleotides, that are rather complex molecules) better than the other "billard balls" in the primordial soup, meaning that RNA subunits would bind preferentially to these minerals, which would hugely increase the likelihood of polymerisation. The fascinating thing being, that once an RNA molecule of some length is assembled, it has been shown, that it (like DNA) can act as a template for creating a new (complementary) RNA molecule. Only this template action is likely to be with a MUCH greater specificity than the binding to the mineral.

Chemical reactions depend only on three things:
Activation energy (varies from reaction to reaction)
Location (the entities have to be adjacent to react)
Orientation (The reacting part of the entities have to be placed in close proximity. This is of course more important the bigger the entity is)

A catalyst (for example the clay mineral in question) can influence all three of these parameters making a reaction several orders of magnitude more probable, than if the reacting entities were floating around at random.

Fascinating Prebe.

And if nothing else, at least possible.

--A

Oh yes. Very possible

Fist wrote:Do fragments of RNA exist, just hanging out, doing not much of anything, free to join with other fragments of RNA?

Not much extracelular single stranded RNA in this day and age. The world abounds with RNAses (enzymes that break down RNA). So much of it around, that when preparing DNA from cells, in the old days, you just tipped the tube to make the liquid come into contact with your finger, and within minutes the solution was virtually RNA free because of the RNAses on your skin. This is why it takes extreme care to prepare RNA from cells in the lab (the first 6 months of my PhD was spent learning to do just that )

Prebe wrote:Many of the links I posted contain detailed chemical descriptions of reactions, and I honestly don't understand all the details (at least not without a lot of looking up and intense study, that I am not going to put in). However, I have so much faith (yes, I said it) in my fellow scientists, that I believe in the conclusions a chemist, an astronomer or a physicist draws from their research.

There is a limit to what everyone can understand. My question is: should we all, when we hit our separate limit, start believing, or should we take someones word for it? Someone who are likely to know a lot more about it than we do ourselves?

And this, I believe, is really the crux (again pardon the expression) of the discussion: Do you trust the scientists at their word, assuming that they constantly do all within their power to prove or disprove their hypotheses using the latest scientific tools? (knowing that they may be wrong, but have at least ACTIVELY looked for an answer)

But then you risk falling into a subtler, but no less real trap... I assume you know that many published papers, on all sorts of scientific journals, including Science, are sometimes wrong (in that the scientist get to the wrong conclusion from the data they have) or in extreme cases, pure crap (in that the scientists make up - yes, make up! - the paper)?

I'll mention two cases which could be interesting... The first one I heard about a few years ago, the second is happening as we speak.

1) A few years ago, there was a respected scientist, a geologist among other things, who was known for producing beautiful, intriguing, landmark papers with astounding frequency. He described in very elegant ways all sorts of stuff, producing theories that fascinated the other scientists in his field. The problem was, no one was able to reproduce his data, but most assumed that was because he had (intentionally or not) withheld some crucial technique out of the published papers (he was under contract with a scientific company, more on this later). Then, at some point, he had submitted two papers to Nature (or Science, one of the two), one two months after the other; the reviewers read the papers, and noticed that he had used the same graph to describe two totally different things in the two papers. In the end, it turned out that he had completely invented much of what he had published, simply because the company he was in pretended results.

2) Woo Suk Hwang, the South Korean stem cell researcher who suffered a scandal a few weeks ago because it was discovered he had taken oocytes from two of his researchers for his experiments, published a landmark paper on Science, in June, about how he had produced eleven stable stem cell lines from patients with several diseases. The implications were enormous: if you can do that, you're one step closer to gene-engineering the cells to remove the disease and then transplant them back to heal the person. Enormous.
Except that... well, first of all, within the paper he speaks of producing a stem cell line "with the genetic imprint of spinal cord injury" among the various "diseases" he has used. He even goes on to say that all these cell lines (including this one) cannot be transplanted back because "they still bear the genetic marks of the disease". How can that be possible? Spinal cord injury is - as the name says - an injury: your spinal cord breaks. That's it. There is no gene or set of genes that suddenly causes your spine to break, or that makes you susceptible to spinal cord injury more than the average person. And the researcher didn't mention any particular genetic condition that could lead to spinal defects - he clearly spoke of "spinal cord injury". So how come he could have cells with a genome that could "produce" spinal cord injury?
As if it were not enough, it turned out a few days ago that one of the pictures he submitted with the paper - well, it was accidentally duplicating. Instead of showing data about the 11 cell lines, the picture showed the data from two or three of them, repeated four times, but strangely, named with all eleven cell lines.

Nowadays science is becoming strangled by companies - research has become a minefield. If you discover something great - you immediately patent it and make your own company; and if you belong to a company and make a discovery - the company has the last say as to what you can divulge, including the methods you used. Without clarity of methods, your results cannot be reproduced, and so you could publish all sorts of false data, and few could tell the difference, if any.

If you want another example, people in my lab once needed a DNA vector from a company. The company said it would be willing to sell it to them, but on condition that they would sign an agreement with the company, which would not only prevent them from giving samples to other scientists outside of the lab, which would not only force them to acknowledge and thank the company in any paper they published using this vector, BUT which would force them to submit papers to the company's board BEFORE sending them off for publication, and which granted the company's board full power to veto a paper, if they didn't like it.

The point I try to make is, once science was much more free, and now it's being strangled by companies and private businesses. Whenever such a situation occurs, sometimes truth is sacrificed for financial gain: this happens with discoveries as well. So, taking all discoveries and papers at face value is in its own way as dangerous as it is stopping looking for answers.

Prebe wrote:Or do you believe, that we have found out all that is to know using present scientific methods, and any explanation before that can be conveniently ascribed to a higher power?

What I am saying is: The point where you don't personally understand anymore, is not necessarily the point where you should start believing. But the moment you start believing could be the moment you stop looking for answers.

I think here there is some confusion between faith and intelligence. Just because one takes a few things by faith (for example, that God exists) doesn't necessarily mean you immediately turn a blind eye to everything else. Yes, some people - far too many - end up doing exactly this, but by no means everyone, or you wouldn't have scientists with any faith I like to think of the Universe as a huge puzzle (in my personal case, I believe Someone made that puzzle, but you of course might think it differently); the fact that I believe doesn't mean I stop looking for answers - it just changes my perspective. We both want to solve the puzzle, though. As I said earlier, I don't believe that the Bible says the literal truth - it's more likely to me that it is allegorical.

Hmm.... strange. It appears that my last post wouldn't show up until and unless another post was made... sorry for the double posting, then, but it was necessary for everyone to be able to access my post!

That sometimes happens, Xar. I've seen times when at least three or four posts don't show up. When you're looking at thread names, see that someone is listed as the last poster of the thread, but that post doesn't show up when you go into the thread, just hit the postreply button. Any posts that didn't show up since the last visible post will be there. Eventually, it fixes itself.

Menolly wrote::::I am so lost:::

:::sigh:::

I really did try keeping up with you guys...

Skin of my teeth! For me, this thread is a perfect example of the old saying: The more I learn, the more I see how much I have to learn. Or however it goes.

Xar wrote:But then you risk falling into a subtler, but no less real trap... I assume you know that many published papers, on all sorts of scientific journals, including Science, are sometimes wrong (in that the scientist get to the wrong conclusion from the data they have) or in extreme cases, pure crap (in that the scientists make up - yes, make up! - the paper)?

I know that some scientists cheat and make up results. Does that mean you never believe a scientific article unless you have the raw data to analyse yourself? And how about papers where the raw data would be greek to you or me? Do you always disbelieve them?

I am always carefull when papers are worded to certainly, but generally I believe what scientific papers in high impact journals say. Especially when it comes to several persons having done the same (or analogous) work, and that is collected in reviews.

Xar wrote:How can that be possible? Spinal cord injury is - as the name says - an injury: your spinal cord breaks

Perhaps a cromosome broke too ?

Xar wrote:The point I try to make is, once science was much more free, and now it's being strangled by companies and private businesses. Whenever such a situation occurs, sometimes truth is sacrificed for financial gain: this happens with discoveries as well.

Couldn't agree more. And for the simple opportunity of getting a job. In Denmark it is almost impossible to get a phd. scholarship (let alone a job) without at least three publications under your belt. I have often thought of (but never did) how easy it would be to produce some plausible results.

Xar wrote:So, taking all discoveries and papers at face value is in its own way as dangerous as it is stopping looking for answers.

Again I agree, but there are fields where, due to your non-omniscient education, you have to take the conclusions at face value. I refer you to my above paragraph (about more person having done analogous work).

Xar wrote:I think here there is some confusion between faith and intelligence. Just because one takes a few things by faith (for example, that God exists) doesn't necessarily mean you immediately turn a blind eye to everything else. Yes, some people - far too many - end up doing exactly this, but by no means everyone, or you wouldn't have scientists with any faith I like to think of the Universe as a huge puzzle (in my personal case, I believe Someone made that puzzle, but you of course might think it differently);

I have absolutely no doubt about your intelligence, or about the existence of intelligent religious scientists. But I ask you again, using your own parable: You want to strive to find out how the pieces of the puzzle fit. But wouldn't you agree, that as a religious person you would have to say that God made something?. In other words if you had the tools, would you strive to find out how the pieces were made? An example: Let's say that you think God made nucleotides, or that God assembled them. Would you try to find out if there was a way they could have been assembled without the aid of God? As a scientist you should.