Make Fist a believer!!! heh

[Avatar]

What I was trying to hint at is that...complexity existed even in the most primitive lifeforms.

Aah, that's where I thought you might be headed. I think you did an excellent job of not inserting any subjective opinion into that explanation, which is why I wanted Prebe's input too, for the simple reason that I know he shares my own viewpoint, and I was hoping for some "evidence" that supported my thought that it is all pretty much random.

Fist..."holographic" information system may or may not be something real...what I was talking about was based on the lines of how every bit of a holograph contains the entire image. If you take a rock, and smash it up, every bit of the rock is still a rock. So in essence, a rock contains all data about itself in every part of the whole. (Clearer?) Anyway, v. busy, will be back to this thread as soon as I can.

--A

[Prebe]

What I was trying to hint at is that...complexity existed even in the most primitive lifeforms.

We don't really know do we? After all, the only info we have on the first cyanobacteria is skidmarks on a few rocks, we can only guess about what preceeded. But even if the first observed (observed is the keyword here) cyanobacterias had fully developed replication/synthesis systems as the modern ones do, it really wouldn't be that strange. What is (of course) most represented in the fossil record is organisms that were plentyfull (a good reason that the so called transitional forms are rare in the fossil record).

My guess is, that the organisms did not really become plentyfull BEFORE a signigficant degree of complexity in biochemical systems was reached, which is one of the reasons that you don't see much evidence of anything before the first cyanobacteria. And again, how can we know, how advanced their biochemistry was?

In short, biochemical complexity (call it completeness) in the early organisms of the fossil record is hard to demonstrate. And even it could somehow be demonstrated, it would not be hard to immagine why the progenitors of these systems do not abound: they were not effective yet.

So, in my view, what we conceive as early biochemical complexity does not constitute a reason to believe in divine creation.

[Prebe]

As for the plasticity and interchangeability of genomes that Xar mentioned earlier:

MAMMALIAN mitochondria! DNA sequences evolve more rapidly than nuclear sequences. Although the rapid rate of evolution is an advantage for the study of closely related species and populations, it presents a problem in situations where related species, used as outgroups in phylogenetic analyses, have accumulated so much change that multiple substitutions obliterate the phylogenetic information2. However, mitochondrial DNA sequences are frequently inserted into the nuclear genome3, where they presumably evolve as nuclear pseudogene sequences and therefore more slowly than their mitochondria! counterparts. Such sequences thus represent molecular 'fossils' that could shed light on the evolution of the mitochondrial genome and could be used as outgroups in situations where no appropriate outgroup species exist. Here we show that human chromosome 11 carries a recent integration of the mitochondrial control region that can be used to gain further insight into the origin of the human mitochondrial gene pool.

[Xar]

Let's talk

How about you talk, and I'll go *bbbbbbbbbbbbbbbbbbbbb* with my finger on my lips.

I haven't read much of Genetics for Dummies yet, so I really don't have much of a grasp on DNA, and even less on RNA. From what you're saying, I guess RNA is assumed to be a precursor of DNA?

Well, that's a complicated question... many scientists currently believe that RNA came first, and DNA only appeared later. This would also stand to reason, as RNA is a single strand (whereas DNA is a double strand) and is all in all a simpler molecule. However, nowadays RNA is not a precursor of DNA - but it has taken on a variety of functions in the living cell. The most well-known is that of a messenger: when a protein needs to be synthetized, the information codified in the appropriate DNA sequence is copied into a RNA template, which then leaves the cell nucleus and goes on its merry way to provide ribosomes with the instructions they need. But RNA is also present in other parts of the cell: ribosomes themselves, for example (the enzymes which translate the information codified within the RNA messenger into a protein) are partially made of RNA.

And this mechanism seems to be more ancient than the now common enzymatic catalysis mechanism.

What does this mean? "Seems to be"? How can such a thing be determined? Is it at all possible to explain in lay-terms?

Well, admittedly, it's kind of hard to find fossils of RNA strands But RNA-mediated catalysis is the simplest kind of catalysis known to us: furthermore, it appears to be conserved even now (there are a few cases in which some cells relies on RNA catalysis), it is relatively inefficient but it does not require any other molecule but RNA itself and the "building materials" for the reaction it has to catalyze. Furthermore, this RNA can replicate itself, albeit with lower efficiency than today's DNA replication: so, it is conceivable that a purely RNA-based organism existed, and such a lifeform would be much more primitive than the old theory that the first lifeforms already included RNA (or DNA) and proteins and enzymes. The latter could have arisen later, but evolutionary biologists are mostly persuaded that there is evidence enough that the Earth was a RNA world at the beginning of life.

At the same time, RNA is more unstable than DNA, so it was not only more at risk of mutations, it was also more at risk of damage - so it converted to DNA, very probably exploiting some of the first primitive proteins as well. And from there, well, there we began to see an explosion of complexity. DNA was more stable, so it could allow itself to be bigger; it could also produce RNA, which would catalyze more primitive proteins; and some of these could help the DNA replicate itself, or even produce more proteins!

I get lost after the word "bigger." But why wouldn't the relative instability, and therefore greater rate of mutation, of the RNA more readily allow an "explosion of complexity"? Isn't mutation what determines such a thing?

Well, in a way you are correct - the higher mutation rate back then - with the lack of protective systems - surely enabled the primitive RNA molecules to "evolve" much more rapidly. But consider also that mutations could have been equally likely to destroy a RNA molecule altogether, or make it unable to catalyze reactions (and therefore ultimately dooming it to "death"). That is why eventually life switched to a DNA basis - being a double-stranded molecule, DNA is inherently more stable than RNA, and if a mutation occurs on one strand, you can use the other as a template and repair the mutation, in most cases. And even if you can't, when the DNA replicates itself it "opens up" and splits into its two strands, each of which is used as a template for the formation of the other strand - so in the end you would obtain a flawed DNA molecule and a completely "healthy" DNA molecule - thereby preserving the information held within.

So after a while our primitive life forms were floating somewhere, little more than a lipid membrane full of water, amino acids, proteins, ions, and long strands of DNA and RNA. Mutation is still a factor - there aren't likely any means of protecting DNA safely - so the life forms diversify. And sometime later, one of these life forms developed a better way to produce energy. And another, passing by, ate the first one - but didn't digest it, it simply held it within, drawing on the energy it would produce. In time, the first life form would become the progenitor of mitochondria

I remember hearing about mitochondrial DNA a few times. A show on PBS or the Discovery Channel, The Real Eve, said (iirc) it is not the same as the DNA of the rest of the organism. What's more, it passes through the maternal line, allowing us to follow genetic lines fairly easily. I guess the mitochondrial and the other DNA are synchronized, so that they both reproduce at the same time? Otherwise, the cell would divide, and only one of the daughter cells would have mitochondria? But maybe that's not a good guess (or, more likely, a complete misunderstanding of the process), because that couldn't have been the case when the one life form ate the one that had better energy production. *head spinning*

Prebe explained this already, I think

and this is a process that japanese scientists have reported to be happening now in another micro-organism in Japan!

That's cool news to hear about! And it also brings up a point. As the theory goes, when, for example, geographic isolation of a group of members of a species occurs, and the isolated group eventually evolves, the larger group is still around also, and has possibly evolved in a different direction. So there's now two species running around. In a part of your post that I snipped, you said, "Indeed, it is believed that the first life forms were RNA-only: at first, it was just as a template for replication, but then slowly this template evolved..." So then are there still RNA-only life forms running around??

Prebe explained this, too

if you compare the genetic codes of eukaryotes and prokaryotes

Oh!! I read about them today!! Eukaryotes have a nucleus, where the DNA is; prokaryotes do not have a nucleus, so the DNA floats in the cell's cytoplasm. Yes?

Exactly; in other words, we are eukaryotes, while bacteria are prokaryotes. The eukaryotic genome is also much bigger than a prokaryote's, and much more complicated as well. Just imagine that if you took out the DNA contained within a single cell of yours and you stretched it all into a string, attaching chromosome to chromosome, you would get a DNA molecule long enough to get to the moon and back...


If you are interested, here's quite a bit on the RNA world theory, as described by one of the scientists who first proposed it (be warned - it's quite a long essay, and possibly parts of it are fairly technical!):

www.geocities.com/CapeCanaveral/Lab/2948/orgel.html

[Prebe]

Another good post Xar (we are turning into the gruesome two-some). One slight correction though:

furthermore, [RNA-catalysis] appears to be conserved even now (there are a few cases in which some cells relies on RNA catalysis)

Wouldn't you say that protein synthesis in the ribosomes is, at least partly, depending on RNA catalysis (ribosomal RNA)? And protein synthesis, being common to all life today, makes RNA catalysis universal?

The question being of course whether this RNA-catalysis is a NEW adaptation (apomorhism), or whether it is a remainder of an ancient RNA catalysis system (plesiomorphism).

Edit: The DNA from one human cell is about 1 meter in length when stretched. I think the calculation you are thinking of is when DNA from all cells in the body are combined.

2nd. edit: re. RNA-catalysis: The article you linked to claims:

Harry F. Noller, Jr., of the University of California at Santa Cruz has found that it is probably the RNA in ribosomes, not the protein, that catalyzes formation of the peptide bonds.

Another good support for the existence of RNA catalysis. The question is still whether this trait is apomorphic or plesiomorphic.

[Avatar]

Oh boy, I can see this thread getting very confusing. But WGD's all around for our geneticists. Very interesting guys.

--A

[Prebe]

C'mon AV! You've followed worse than that. Remember your inbreeding genetics 101

[Avatar]

Oh, I'll be trying to follow and asking questions, just don't have the time to spare today. Thankfully, next week is set to be a lot quieter for me, and I'll be paying close attention.

--A

[Fist and Faith]

Allright, first of all let me add one more fact to the idea of DNA as an information system that has been floating through this topic. Until a few years ago, it was believed that all of our DNA would codify for proteins - then, it was discovered that actually the greatest part by far of our DNA is silent - it is not translated into proteins, and seemed to have no particular function except sitting there and taking space in the nucleus. Still, well, you have some codifying DNA, so at least the one gene - one protein axiom works, right?

Well... no. It was later discovered that most genes have the capacity to produce more than one protein, by "splicing" the RNA transcripts they produce. So, if you have a gene which codifies for the protein ABCD, chances are that it could also codify for ACD, ABC, BCD, or even just C. A complex - extremely complex series of mechanisms regulates which proteins are produced in any given moment, and in which quantity.

Then it was discovered something even stranger: in some cases, there are genes that can produce more than one protein, and to produce some of these proteins they skip the "STOP" signal and utilize some of the supposedly unused DNA!

And then another discovery - there are pieces of supposedly unused DNA which can "jump" from gene to gene, or even from chromosome to chromosome, detaching from a DNA strand and attaching themselves to another, often causing mutations!

And this only scratches the surface of what is actually going on inside us... So, as you can see, the picture is much more complex than first thought.

This is an incredible few paragraphs! Without having any true understanding of what you're saying, I recognize the complexity and bizarreness of it!

Now on to Avatar's post. It is undoubtly true that the first lifeforms were nowhere near as complex as we are. But there are now serious doubts that life began with proteins in the first place.

How sure can we be that RNA is the real beginning? I don't imagine there's any real way to test the theory. Is it more like keeping an eye out for any current events that show we misunderstood how RNA behaves, and therefore how we assume it behaved back then?

And even though I imagine the answer is in there amongst everything you said, let me ask anyway... Is the change from thinking that it was protein to thinking it was RNA merely another step back in time? Or is it an entirely new theory? If RNA plays a role in the production of protein, then the theory has merely been - refined?

The interesting observation you raise, about whether DNA is a lifeform by itself, is actually an intriguing bone of contention among a few biologists right now. From a certain point of view, if you think about it, all living beings exist to perpetuate the species - therefore, to perpetuate their DNA. You might even go as far as claim that the human body is an appendage of DNA - a sack full of seawater that DNA uses to go around and propagate itself. "The selfish gene" is a book which explains this point of view.

I've heard it said that the body is the brain's appendage, but the DNA idea is even more interesting!

[Gadget nee Jemcheeta]

That's a little disturbing actually. My identity as a sack of seawater :p

[Fist and Faith]

I think it teaches us some needed humility.

[Gadget nee Jemcheeta]

You would! You and your humility...hmmph...me and my ego will be in the corner, if anyone needs us.

[Avatar]

Good post Fist, and the one of the very things I was wondering. There must have been RNA precursors as well, surely? Even if just simplified, minimally functional versions.

I do tend to think of my body as my brains appendage, and the whole idea and progression of intelligence is one that fascinates me.

But that's not the point of this I guess.

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.

If the base point is sufficiently simple, then it's quite feasible that no design is required, that the natural progress of mutation and adaptation simply increased the complexity, added redundancy, etc.

An interesting question would be how much of that superfluous DNA material we can do without.

We also neglect the fact by virtue of the conditions under which we evolved, the human body, for all it's toughness and adaptability, is biologically, especially biochemically, a fairly fragile system. For example, a simple thing like dehydration upsets the slat/water balance of your body, and if not rapidly counteracted by adding water, leads to organ failure and death.

Our range of survivable temperatures is pretty small as well, all obvious signs of biochemical adaptation to a specific conditions, at a specific time.

--Avatar

[Xar]

On the other hand, the human body isn't as fragile as you think... dehydration is a danger for every creature, because our chemistry is based on water; but the human body (or any other animal's) is extremely adaptable, biochemically speaking. There are whole biochemical pathways which, even if blocked, despite their importance, do not necessarily lead to death, because other, perhaps less efficient but nonetheless existing pathways will take up the burden. It's a similar principle to the dominant/recessive system in genetics; even if an allele of one of your genes is defective, the other one could have an effect large enough to "cover" the defect.

Indeed, we have even ways to repair our own DNA if it suffers damage - even damage as tiny as the loss of a single base! It would be as if we were constanly running spelling checks on the Bible and correcting any printing mistake we would find. Granted, a few of these systems can cause other mutations, but several have proof-reading capabilities and lead to functional recovery.

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

[Avatar]

Wow, a single cell? Awesome. Thanks for the links.

OK, maybe "human body" should have been replaced by "life' instead. Regardless of the back-ups though, regardless of the adaptability, of the small fixes (or defenses) that the body can muster to protect itself, don't those only work in limited ways? It doesn't take much to end life afterall, a few hours at temperatures significantly higher or lower than opitmal can be enough.

Still, we're getting off the track here I think, because you clearly don't think that man was created whole and "as is" at the beginning of the world, and on that, I very much agree with you.

What I'm after here is similar to Fists desire I think...is it possible, (not likely, not probable, but possible) that the complexity evolved, that the less complex attempts have simply faded into the void of the past without being recognised or noticed, and that DNA has become what it is, from something much much less, over a long period of time?

In other words, is there an explanation that allows for the possibility that it (the complexity of DNA), didn't have to be designed?

I doubt that there is, but then, I equally doubt that there's any evidence that it did have to be designed.

Afterall, if RNA became DNA, then DNA wasn't simply slotted into place ready-made. And the simple fact that primitive life-forms were "coded" by something other than DNA doesn't make it unreasonable that something preceded that, which became RNA, and so on, back to some acceptably simple form, with only the bare minimum of processes to sustain some semblance of "life".

--A

[Xar]

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.

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.

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? 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.

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. 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...

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.

[Avatar]

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?

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.

That is pretty much the argument I would use, especially given that it has been demonstrated that such "building blocks" can be produced by the conditions extant at the time. Afterall, in theory, the argument is perfectly valid, isn't it? Remember, I'm not concerned with the improbability here, only the possibility.

If natural conditions could produce the building blocks of RNA, then it is possible that natural conditions eventually permitted/encouraged that binding, and that "bending."

As for the fragility, I certainly agree that the more complex life is, (i.e. the more things that can go wrong), the easier it is to destroy any given individual. And I also agree that the incredible tenacity of life means that it will almost certainly survive in some form.

--A

[Prebe]

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’ll have to quote myself here (sorry):

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.

[Avatar]

Hmm, forgot that you'd said that...

Do I understand correctly that you suggest that it's possible that by filling the pre-existing grooves, the components were "forced" into that shape?

--A

[Prebe]

Yes. Or more corretly, they were forced into close proximity to each other by abiotic factors, perhaps even with the right orientation. This greatly facilitates the formation of bonds between subunits.

Immagine the probability that two billard balls in motion meet by accident on a pool-table. Now immagine the same two balls meeting if you place them in a rain gutter. Actually the billard balls (subunits) would have to be moving in three dimensions (in a primordial soup) and not just two, which means an even larger relative increases of reaction probability (bond formation) in the rain gutter.

This is a spatial problem and hence very hard to describe to a person who can't form images in his mind