Ribose Optimal?
by BilboI imagine that in one of his two upcoming volumes, Mike Gene will discuss whether DNA and RNA were optimal design materials. When I read Robert Shapiro's comments that Mike linked to here:
http://www.edge.org/documents/life/Life.pdf
I found this:
There's famous set of experiments from about ten years ago when Albert Eschenmoser, a brilliant Swiss synthetic chemist, set out to prove why
nature had a select DNA. With enormous Swiss skill and manpower he set
students out to make DNA-like molecules using different sugars, one after the
other, expecting that in every instance he would fail. But in fact he succeeded and
he found that different sugars in many cases was superior to DNA. They had
greater stability; they had fewer complications in replication.
I thought that he would arrange to have the Swiss government declare that from
now on every Swiss life form would adapt his symbiosis and dispense with DNA
as quickly as possible. There's PAN, and someone else came up with TNA "”
there's endless ones "” and so to me DNA is probably what evolution stumbled
upon through accident, and it's the easiest thing that could be come upon by slow
trial and error that would make a molecule that could be replicated by proteins
and that's how it came into being.
If Shapiro is correct, I think this would be quite a challenge to ID. So I've started looking to see if I could find more on this. So far, all I've found is this article:
http://discovermagazine.com/1993/aug/unnaturalacts254
which suggests that ribose and other pentoses are optimal. Since I know next to nothing about chemistry (or science), I thought I would just toss this out there to see if anyone else knows more about this.
But let's keep it confined to RIBOSE or the other sugars. Mike has already addressed cytosine in his book.
May 10th, 2008 at 6:27 pm
Bilbo, thanks for the interesting post.
I asked Mike in a previous thread (the one in praise of proteins) a very related question:
Unfortunately, Mike didn't answer (Mike usually ignores me; boohoo). But it appears that in the case of DNA, rather than proteins, someone has actually tried to figure out if DNA is optimal in some way. This is of course a very difficult problem, because it is not so evident what function of an hereditary molecule is expected to be optimized. Stability? Copying-fidelity? Or even evolvability? The latter could be considered a FL criterion. It appears that DNA is at least not optimal in the stability department.
[edit: sorry, I didn't see in time that you wanted this thread to be confined to sugars. Delete this if you want]
Comment by Raevmo — May 10, 2008 @ 6:27 pm
May 10th, 2008 at 6:51 pm
Actually optimality is a basic principle of protein design (evolution), Raevmo.
The difference is that a "hereditary molecule" is optimized wrt an arbitrary (a priori and independently given) evaluation of its "fitness."
Whereas in protein design that problem is transferred back onto DNA. (So proteins, derived from DNA, can be evaluated as "fit" if they minimize an energy function, or some such related function.)
See what I'm saying?
Comment by Rock — May 10, 2008 @ 6:51 pm
May 10th, 2008 at 6:54 pm
The underlying question was not if the structure and function of proteins is optimized, but rather if the material to make proteins is optimal. I.e. might there be a material that would work better than the most commonly used 20 amino acids to perform the function of proteins as we know them
Comment by hrun — May 10, 2008 @ 6:54 pm
May 10th, 2008 at 7:15 pm
Rock:
I think so, but I think you missed my point. I wasn't talking about proteins being optimized wrt their amino acid sequence in order to minimize some energy function. I can see how that works. I was looking at optimization wrt a much a larger space, namely the space of all potential monomers. What collection of monomers (such as the 20 standard amino acids or perhaps something entirely different) makes for an optimal system of polymers? I asked this because it was my impression that Mike Gene was rather impressed with the wide range of functions being performed by proteins (and indeed it is impressive), and he seemed to consider this as an optimality property of proteins, compared to other potential polymers consisting of different monomers. One would expect a Designer to pick an optimal collection of monomers, but I am not aware of any evidence supporting the idea that the 20 amino acids are such a collection.
Of course, but the difficult question here is how the properties of different types of hereditary molecules map onto fitness. Is it just stability? Probably not.
[edit: I see hrun beat me to the punch]
Comment by Raevmo — May 10, 2008 @ 7:15 pm
May 11th, 2008 at 4:00 pm
The Discover article also talks about alternative proteins, but let's not discuss them here. I can always start another protein thread, if you want.
Meanwhile, here's what it has to say about sugars:
Comment by Bilbo — May 11, 2008 @ 4:00 pm
May 11th, 2008 at 4:40 pm
I'm finding a number of interesting abstracts, but without a subscription, this could be very costly.
Comment by Bilbo — May 11, 2008 @ 4:40 pm
May 12th, 2008 at 3:51 pm
A gradual accrual of ribose ultimately yielding RNA isn't very plausible. Ribose is an unstable sugar (like most sugars) because of the (OH) grouping at the 2' location on the sugar (opposed to just the H on deoxyribose). Even in a neutral solution ribose (and other sugars) have a very short half-life.
The reaction that yields ribose, the formose reaction, yields other sugars as well with no bias towards ribose formation. The consequent polymerization of sugars is nondiscriminatory…. so there's nothing from preventing ribose to bond with other, random sugars produced from the formose reaction.
So, this ribose has to somehow survive the struggle to get to the level where it can wear both hats (information carrying macro-molecule and catalyst).
Comment by Doug — May 12, 2008 @ 3:51 pm
May 12th, 2008 at 4:31 pm
Shapiro cites Eschenmoser's work to show that DNA made with other sugars is better, allowing Shapiro to conclude that ribose was a suboptimal, frozen accident. The only full paper I've been able to read suggests that ribose has more efficient replication properties. I'm unable to find anything else, except abstracts. But it sounds like Shapiro may have been relying upon Eschenmoser's earlier work(?).
But what I find significant about Eschenmoser's work, is that with Mike Gene's front-loaded evolution hypothesis, we have a hypothesis that can be tested. One could go into the lab and test whether the basic materials of the cell are optimal in the sense needed for Mike's hypothesis. And this can be done by substituting different chemicals. Different sugars and nucleic acids for DNA and RNA. Different amino acids for proteins. If the substitutions work better than the original material, this would weaken Mike's hypothesis. If they don't work as well, this would strengthen it. Of course, we should specify in what way we mean "better."
Comment by Bilbo — May 12, 2008 @ 4:31 pm
May 12th, 2008 at 4:33 pm
Bilbo, post a link using your search terms in Google Scholar and which extracts look most promising and I'll be glad to send you a few copies.
Comment by todd — May 12, 2008 @ 4:33 pm
May 12th, 2008 at 4:35 pm
But how would a suboptimal design actually argue against ID or front-loading. That would be like arguing that the Edsel was not designed. At least that (or something similar) is what ID proponents often say: lack of optimality can not be taken as indication of no design.
Likewise, I would guess, there is no reason to believe that nature can't come up with optimal 'designs'.
What are your thoughts on this?
Comment by hrun — May 12, 2008 @ 4:35 pm
May 12th, 2008 at 4:52 pm
Mike's hypothesis assumes that the designers were smart — not likely to come up with stupid design solutions. An occasional goof wouldn't falsify his hypothesis. But if we find mistakes over and over again, non-teleological evolution becomes the stronger option. And if we find mistakes in the most basic and important materials, even one goof becomes a serious challenge to Mike's hypothesis.
Yes, I agree. But we think of nature coming up with optimal designs on a trial and error basis. If nature gets it right the first time, every time, I think we should be suspicious. For example, if Ribose is a frozen accident, that nature just happened to stumble upon the first time, that's quite a bit of luck. If we find out that other frozen accidents are also optimal — the genetic code, the amino acids, the nucleic acids — I think that tends to strengthen Mike's hypothesis.
But could nature have been experimenting with different sugars before settling upon Ribose? Sure, I guess (not sure how likely it is to get any sugars). But if that's what happened, would it be unreasonable to think that there are remnants of the precursor sugars someplace it nature? Are there any ancient organisms that are still using one of the other sugars? Or must we rely upon a hypothetical, pre-Ribose world? It's possible that that is what happened. But again, what if it turns out that we must constantly rely upon such a hypothetical world for all of nature's early experiments (with proteins, DNA, RNA, the genetic code)? Then I think we are in a position where some of us would prefer relying upon a hypothetical designer, and seeing where that hypothesis takes us.
Thanks for asking. Do they seem that unreasonable?
Comment by Bilbo — May 12, 2008 @ 4:52 pm
May 12th, 2008 at 4:55 pm
Thanks, todd. I'll give it a shot.
Comment by Bilbo — May 12, 2008 @ 4:55 pm
May 12th, 2008 at 4:57 pm
Hi Bilbo,
Was the pathway to the sugars one found in nature?
Or did the students play the role of selective filter opting for the sugar they wanted to test? If these are sugars that are typically produced in the formose reaction then there still exists the obstacle of weeding out one particular sugar from a process that isn't selective with the sugars that it yields.
Also, when they say that these sugars are more stable than ribose that still isn't saying much (until we know their exact half-lives) because depending on the temperature and pH of the solution you have a half-life of ribose that ranges from 3 hours to 50 years.
Even with a process that only yields ribose (or their sugar of choice) in a pristine environment void of interfering reactions, that half life doesn't bode too well for the longevity for these monomers.
Comment by Doug — May 12, 2008 @ 4:57 pm
May 12th, 2008 at 5:07 pm
Running out of time, Doug, so I can't even read all of your post. Here's a paper to start with:
http://structbio.vanderbilt.ed...
Comment by Bilbo — May 12, 2008 @ 5:07 pm
May 12th, 2008 at 9:00 pm
Are you saying that the folks who designed the Edsel were not smart? It's also worth considering that 'good enough' is the hallmark of efficiency. So maybe a designer might not chose the optimal material but the one that will suffice. In fact, wasting time for searching an optimal solution when a usable one is already at hand would be a sign of a not so 'smart' designer.
Let's face it, Bilbo. We can't really make any statements about a 'designer' who we don't know– other than that he must be capable of designing something and implementing that design. That's all. Maybe it was a little alien nine-year old who designed humans as a science project, pulling an all-nighter with a little help from mom. Maybe the life created by the 'smart' alien is infinitely more efficient than human beings. I mean, really, who knows what a designer would do and would be capable of.
Not clear that nature must get it right first time around. It might develop many possible solutions in parallel and the best one might win out. Also, things are apparently not immutable. For example, it appears that ribose was the earlier sugar used. Nature apparently then switched to using deoxyribose to optimize for stability.
Not all of them. But the assumptions about the designer do seem unreasonable. On the other thread I have been arguing with folks who apparently can't even agree if the designer itself lies within our without science (the physical world, …). Apparently that leaves open aliens, all sorts of deities and of course the christian god. That's such a huge range of potential designers, some of them way beyond inquiry, that I don't think you can make any assumption about the designer.
Unless of course you have a specific theory about the designer. Which would be great. Because then we could test if it was possible that such a designer, with those characteristics was present at the time of life's appearance on earth. We can test if he had the means to actually create life on earth. And so forth… you know, how archeologists and forensic scientists deal with 'design theories'.
Comment by hrun — May 12, 2008 @ 9:00 pm
May 13th, 2008 at 3:54 pm
Not sure. Are there natural (non-biotic) pathways to sugars?
Comment by Bilbo — May 13, 2008 @ 3:54 pm
May 13th, 2008 at 4:09 pm
How would we know? Even if they occur in space- even from all known organic lifeforms- they might have still been created by an intelligence.
Comment by hrun — May 13, 2008 @ 4:09 pm
May 13th, 2008 at 4:12 pm
Since one of the goals of designing cars is to design one that appeals to the public, no, they were not smart.
Good enough for what? Mike's hypothesis is that the first cells were designed with front-loaded information that would be carried into the future by reproduction. If they were designed with an inferior sugar for that purpose, when a superior one existed, then why not use the better one? And if we can spot the inferior product, when we are only beginning to understand biotechnology, why should we think the first cells were designed by minds supposedly far more knowledgeable in this area?
We can make hypotheses, and then test them. Mike has made a hypothesis: the first cells were designed by an intelligence that had the necessary knowledge and skill to front-load information that could be carried into the future by reproduction, taking advantage of evolution to implement future designs.
If Shapiro had been correct, and hexose-DNA was superior to pentose-DNA, then this would have been a significant blow to that hypothesis.
Yes, that might happen. But shouldn't we expect to see remnants of the other possible solutions somewhere in nature, still managing to thrive in their own little niche? And if we don't find them, are we sure they ever existed? And if we aren't sure, but we keep testing Mike's hypothesis, and we keep finding that the basic materials are optimal, shouldn't that strengthen his hypothesis?
Is this based on the RNA world hypothesis, or do we know this for a fact?
They're part of an hypothesis.
But if you want to be able to test a hypothesis, you must make some testable assumptions.
So if we found that mousetrap on a distant planet, no sense thinking it's designed until we find independent evidence of a designer? Sorry, I don't buy it.
Comment by Bilbo — May 13, 2008 @ 4:12 pm
May 13th, 2008 at 4:18 pm
Are there natural pathways to sugars, where if they were designed by an intelligence, that intelligence remains in doubt by most of the scientific community?
Comment by Bilbo — May 13, 2008 @ 4:18 pm
May 13th, 2008 at 4:24 pm
Hi Bilbo,
Nice thread. You wrote:
Me neither. It goes back to the Face on Mars. I would consider the higher resolution picture as evidence for design even without having a shred of independent evidence of a designer. I suppose some would deny the evidence and demand to see the designer instead.
Comment by MikeGene — May 13, 2008 @ 4:24 pm
May 13th, 2008 at 4:37 pm
Most of "my" thoughts are plagiarized from your book.
Comment by Bilbo — May 13, 2008 @ 4:37 pm
May 13th, 2008 at 5:56 pm
Wow. You are talking about beings that are able to design a car that actually runs and you are telling me they are not smart? That's truly shocking.
Good enough for life? Good enough for 'front-loaded evolution'? Good enough for efficient reproduction? Take your pick?
This whole paragraph does not answer the question: Why do you assume that a designer has to chose an optimal design material? If there is a design material that already serves the purpose of a designer, it is folly (i.e. not smart) to look for one that might be even better at fulfilling that purpose.
And it does not answer why evolution would not find the eventual optimal solution.
Really? Mike made a hypothesis about the Front Loader. Namely that the Front Loader did everything just so that our world looks the way it looks. What else can you say about the Front Loader? And what of these things could be tested?
Again. I don't see how? That's like arguing that the people who made sailboats were not smart designers because steam boats are so much more 'optimal'. In addition, since nobody actually knows what the intention of the Front Loader is, we also can't know if anything that the Front Loader did was optimal to achieve that goal.
What if the goal of the Front Loader was to create life that was somewhat fragile, always in a constant struggle to get by with DNA damage. What if the goal of the Front Loader was to see if one can create life using inferior sugars. Remember that nine year old alien and it's science project? All those aliens use hexose sugars as basic building block. But the project actually was to see if life can exist based on a suboptimal material.
And we do. We, for example, see remnants of RNA as information storage in RNA viruses and telomerase templates. We also see remnants of RNA as catalytic molecule in ribozymes. Maybe you should give nature a little time and it might come up with hexose based DNA. Or maybe Shapiro is wrong. Essentially, the only way Shapiro could be proven right is if he created an organism based on his sugar and looked if it could outcompete other lifeforms.
But how is the hyptothesis about your Front Loader any more plausible than mine about the nine-year old alien and the intergalactic science fair?
Well, that brings me back to my original question: Intelligent Design only makes sense if can actually make testable predictions about the designer and the design process.
But, as far as I understand it, we can't. ID does not even agree on the most basic fact of the designer: Namely whether the Front Loader resides in the physical or metaphysical world.
Nope. We find a mousetrap there then I would guess that humanoids put it there. I know that humans have built mousetraps in the past to trap mice. In fact, I immediately assume that all mousetraps I encounter were built by humans.
Comment by hrun — May 13, 2008 @ 5:56 pm
May 13th, 2008 at 6:04 pm
I found this study: "Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth" (Nature 414, 879-883)
"Here we report that a variety of polyols are present in, and indigenous to, the Murchison and Murray meteorites in amounts comparable to amino acids. Analyses of water extracts indicate that extraterrestrial processes including photolysis and formaldehyde chemistry could account for the observed compounds. We conclude from this that polyols were present on the early Earth and therefore at least available for incorporation into the first forms of life."
So as far as I know we have not found sugar in space, but definitely the building blocks for sugar to form.
EDIT: Interestingly, amino acids were found on meteorites. Isn't it funny that the Front Loader had such luck that the basic building block for the most optimal polymer to create life actually already naturally occurs on meteorites? On top of that we find the precursors to a second basic but optimal building block naturally occurring in meteorites. Think about the odds of that happening twice.
Or maybe the nine year old alien just grabbed everything it had handy in a rush to finish that darn project. Who knows.
Comment by hrun — May 13, 2008 @ 6:04 pm
May 14th, 2008 at 12:55 pm
hrun, instead of going back and forth with this tit for tat, let's go back to what Shapiro thought Eschenmoser had shown — that ribose was an inferior substance. Had this been the case, non-teleologists would be throwing this fact in the face of all of us ID proponents. And with good cause. We claim that the cell is the product of advanced bionanotechnology. But if even we kindergartners in this area can spot a defect, why think it was designed by someone with advanced knowledge? Why not just think that it was produced by the blind watchmaker, who takes whatever substance is available and uses it?
The fact that it now looks like ribose may be an optimal material, means that you have to hypothesize that it was only one of many different experiments that nature tried, and that this one survived.
Suddenly the story changes: From ribose being the first sugar that nature stumbled upon, to ribose being one of many sugars that nature experimented with.
Fine. Change your hypothesis. No law against that. Only now you better come up with some solid evidence that nature did in fact experiment with other sugars. Otherwise we ID critics won't take you any more seriously than you take us.
Meanwhile, ID proponents are taking the risk here. Had ribose proven to be inferior, that would have been a club in the hands of the critics, used over and over again to show how unlikely ID is. And with good justification. The more irrational and lacking in foresight an object is, the less likely we are to think it is intelligently designed.
And as Eschenmoser has shown, there is a way to test ID: go into the lab and try different substances, to see if they work better. Try different pentoses. Try different nucleic acids. Try different amino acids. And either critics or proponents can do this. We finally have a way to start testing ID. Let's use it.
Comment by Bilbo — May 14, 2008 @ 12:55 pm
May 14th, 2008 at 1:06 pm
OK, a little confusion here. Shapiro was referring to Eschenmoser's earlier work (I think), where it appeared that hexose-DNA was superior to ribose. From what I can tell, based on the Discover article and Eschenmoser's latest paper, ribose is superior.
Then I asked if it's a known fact that ribose preceded dioxyribose. And your evidence is viruses and ribozymes. I believe the view that these preceded the present form of the cell is controversial.
Comment by Bilbo — May 14, 2008 @ 1:06 pm
May 14th, 2008 at 1:26 pm
Maybe. But it's stupid to throw this into anybodies face, precisely for the fact that I have outlined: Nobody knows the intentions of the designer and the constraints the designer was under. Therefor, nobody know on what criteria a designer might have chosen the materials.
No, I don't. I say it's a possibility, or nature found it the first time around. Who knows.
Again, how so: Nature is full of what according to some criteria are suboptimal design decisions. None of those count against the presence of a designer.
And again, do you honestly any finding like that would count against ID? The Edsel was clearly designed. It might have had some design flaws, but finding them does not make it any less designed.
It is assumed that ribose preceded deoxyribose. I don't think it's proven yet. But RNA has the odd capability of acting as both information storage and catalytic molecule and is still (at least rudimentary used as both) even though information storage has been supplanted (apparently) by DNA and catalysis has been (apparently) supplanted by proteins.
Comment by hrun — May 14, 2008 @ 1:26 pm
May 14th, 2008 at 5:39 pm
Yes, getting optimal design the first time around is plausible, as long as it is only occasionally. If we find a general pattern, then we either hypothesize that nature experimented numerous times, or we hypothesize a designer. If we go into the lab and experiment for different basic substances — DNA, RNA, proteins — and find that what we are made of is optimal, it weakens the hypothesis that nature got it right the first time.
Sure they do. The backward wiring of the retina in vertebrates is a favorite example of ID critics that it wasn't designed. It appears to be irrational and lacking in foresight.
We have four categories that help us determine if something is designed: Analogy, discontinuity, rationality, and foresight. By and large, ID proponents have confined their evidence to the first two: analogy and discontinuity. But ID critics have retorted that the analogy is weak and discontinuity is an argument from ignorance. So we must turn to the second two in order to help us determine if something is designed. So yes, if lab experiments discovered that there were better ways to design DNA, RNA, or proteins — ways that were more rational and had more foresight — then that would count against design. And if lab experiments discovered that there were not better ways, that would count for design.
I think you're right.
Comment by Bilbo — May 14, 2008 @ 5:39 pm
May 14th, 2008 at 6:31 pm
But you have no way of knowing if nature got it right the first time. This might be the second, tenth or millionth time.
In addition, you still have not plausibly explained why every designer would chose optimal design materials. All evidence we have from human design is that we chose 'good enough' materials that are readily available and not necessarily 'optimal' materials.
You have so many unstated assumption about the Front Loader:
a) the Front Loader is capable of finding the optimal material
b) the Front Loader has the sufficient quantities of the optimal material
c) the Front Loader has the desire to use the optimal material
d) (and this is a really important one) you know what the Front Loader wanted to achieve
I have given you numerous plausible scenarios where none of the above assumptions are true, even if there was a Front Loader.
Can you address any of these points? Can you justify why you believe the Front Loader should actually have acted according all of your assumptions?
So if you believe such examples weaken the design hypothesis, then why are we still talking about it. Design should be dead in the water, since there are literally countless examples such as the retina. So it turns out that suboptimal design is a poor argument, since nobody knows the abilities and desires of the designer.
So I guess it is not sufficient that lab experiments already showed that there is a better RNA: namely DNA and proteins.
Comment by hrun — May 14, 2008 @ 6:31 pm
May 15th, 2008 at 4:48 pm
hrun, it would help a lot if you would read Mike's book.
Mike takes the theory of Darwinian evolution to be true, and that this type of evolution is a very good design mimic. In other words, it can produce things that look like they were intelligently designed. Given that premise, how in the world could we ever tell if some biological feature was intelligently designed? One of the differences is that Darwinian evolution takes what is available and makes use of it. It doesn't matter if it is optimal or sub-optimal. As long as it works.
So if we find an optimal design, we should wonder how nature was able to come up with it. Perhaps nature was experimenting, working with different available options, and the best one was naturally selected. But if that is the case, we should be able to find remnants of the other designs somewhere in nature, that have survived in their own special niches. If not, then how do we know that nature was experimenting? It looks like nature got it right the first time. And this we be suggestive of intelligent design. A designer need not make optimal designs. A designer need not use optimal material. However, if we find an optimal design or optimal material, and no hints that nature had been experimenting, this strengthens the design hypothesis.
The other difference between nature and a designer is that nature does not have foresight. She is just trying to get by for the present time, with no thought about tomorrow. So if we find biological features that seem to show foresight, this also strengthens the design hypothesis.
With both those points in mind, do you still want me to answer your questions?
Comment by Bilbo — May 15, 2008 @ 4:48 pm
May 15th, 2008 at 5:38 pm
Yes. And I have given you MANY examples now where designers do the very same thing: take what is available and make use of it.
Sure. Unless evolution was "experimenting" in parallel and the failed experiments didn't leave remnants. But fortunately, we have such examples: the rather non-diverse catalytic functions or RNA and the excellent catalytic functions of proteins. Or the poor stability of RNA and the high stability of DNA.
Yet, even that doesn't help us much, because the Front Loader could also have experimented, just like human designers often experiment with materials.
And here we come, yet again, to the unresolved problem of what you call optimal. What material and what design is optimal depends on the desire or goal of the designer. What is that goal of the designer that makes this particular design or material optimal.
Obviously you could not argue that, for example, a material can be optimal, irrespective if the goal for the design: For example, if my goal for designing a house is cheapness, then I would probably use slab concrete. If it's supposed to be durability, I might choose stainless steel. If my goal is sustainability, I would chose wood. If my goal would be portability, I would chose nylon.
As I am saying: You are making completely unwarranted assumptions about the designer. You must by argue that the designers goal were actually achieved without knowing what the designers goals were.
Yet again, you are trying to tell me that you know what the Front Loader wanted. The argument is incredibly circular.
Because ribose is optimal for life as we know it, the designers goal must have been that life turns out in the way it did, thus the design of life shows foresight, thus life was designed.
Yes, very much so. Other than pointing out how the Front Loaders experiment actually turned out, can you plausibly explain to me how you know the goals of the designer so you can argue that the design and/or material was optimal to achieve said goal?
Comment by hrun — May 15, 2008 @ 5:38 pm
May 15th, 2008 at 6:05 pm
Yes, designers can do the same thing nature does. What they can do differently is choose not to use what is easily available and choose to use something else.
Yes, if the RNA world theory is correct, then I think this would weaken the design hypothesis considerably. But didn't we both agree that it has been proven, yet?
Yet, even that doesn't help us much, because the Front Loader could also have experimented, just like human designers often experiment with materials.
And that depends upon the hypothesis. Mike Gene's is front-loaded evolution. If the biological feature in question is optimal in regard to that hypothesis, it strengthens it. If not, it weakens it. Had Eschenmoser's earlier work proven correct, and hexose-DNA was better than pentose-DNA, it would have weakened Mike's hypothesis. We could have adopted a different hypothesis, for example, yours about a 9 year old alien's school project. However, most of us would opt for the non-teleological scenario that Shapiro offered. It seems simpler.
Yes, now suppose you use nylon, but we don't know what your goal was. Now Mike comes along and makes the hypothesis that you were trying to design it for durability. Then we (not knowing about stainless steel) discover stainless steel. That would weaken Mike's hypothesis.
Suppose we go into the lab and find a different sugar that would be better at helping the function of reproduction happen (necessary to Mike's hypothesis). This would weaken Mike's hypothesis. We could at that point say that the designer was just using what was available. But then how would this differ from the blind watchmaker? It wouldn't. So it would weaken the design hypothesis.
With both those points in mind, do you still want me to answer your questions?
We don't know the goals of the designer. Mike takes as his starting point that Darwinian evolution is true. Then he hypothesizes that the designer would have used optimal designs and foresight, and exploited evolution to achieve further designs, possible even humans.
If the evidence keeps showing sub-optimal designs, and no indication of front-loading, then this weakens Mike's hypothesis. We could then hypothesize that the designer used sub-optimal designs and no front-loading, but how would we be able to tell the diffence between that designer and evolution?
Comment by Bilbo — May 15, 2008 @ 6:05 pm
May 15th, 2008 at 6:08 pm
And hrun, one further point. It seems obvious to me that you haven't read Mike's book. At this point, I'm finding it difficult to perceive you as a serious investigator into this subject.
Let me say, for the record, that if you only read one book about ID, The Design Matrix should be it. It's well worth the 20 bucks or so.
Comment by Bilbo — May 15, 2008 @ 6:08 pm
May 15th, 2008 at 7:04 pm
So is ribose or sugars freely available to the Front Loader or not? How would you know?
Exactly my point. We don't know what the Front Loader would have done.
So what is the hypothesis? That life was supposed to be exactly like it is? Of course then the material chosen was optimal. Look at that, everything chosen for life fit perfectly to have life come out exactly how it was supposed to come out. Must have been designed.
That's why I asked: can you define independently from the outcome of the experiment what the goal of the Front Loader was? If you are unable to do so, then you are making unwarranted assumptions about if the Front Loader chose an optimal material or not.
Yes, Mike's hypothesis about whether or not nylon was optimal with regards to durability would be falsified. But what else?
I could have chosen Nylon indeed to optimize for durability. Maybe I also was not aware of the existence of stainless steel. Or maybe I chose it for durability and portability. So it might still be optimal for durability, within the bounds of portable materials. Yet again, the falsified hypothesis is not if the 'house' made out of that material was designed, but whether or not you were able to divine the goal of the designer.
What do you mean 'better at helping the function of reproduction to happen'? That is the goal of the designer? The designer wanted to optimize the function of reproduction and thus chose ribose? How do you know that the designer wanted to do that?
And, all you prove if you find that ribose is indeed 'better at helping the function of reproduction to happen', the you still have not advanced the case of there actually being a Front Loader. All you have given evidence for is: IF there was a Front Loader and IF his goal was to find a material that is 'better at helping the function of reproduction to happen' than he did indeed use it for his design.
And wouldn't 'evolution' also want to use the material that is 'better at helping the function of reproduction to happen'?
Mike takes as his starting point that the Front Loader wanted life to unfold exactly how it did unfold. So of course everything we find will be true to that goal, since, lo and behold, life did unfold like it did.
Is there ANY EVIDENCE OTHER than that life happened the way it did about what the goal of the Front Loader was? Anything?
Again, sub-optimal WITH REGARDS TO WHAT? How do you know what was supposed to be optimized. You pick something that you know occurred and then assume that that was the goal of the Front Loader.
Well, that's fine, Bilbo. If you chose only to debate these points with a 'serious investigator' then so be it. I don't think that I should need to read a book in order to understand your argument. If that is the case, though, then I have to say I am disappointed in your ability to argue.
—
Let me just lay out the argument one final time: You make a hypothesis about the goal of the Front Loader. You make this hypothesis purely based on knowing how the experiment (life/evolution) turned out and not on anything else. You then find that the material chosen is optimal in order for the experiment to turn out as it did. And you use this (unsurprising) result to argue that the Front Loader hypothesis is strengthened.
I don't think that this is a valid way to support the 'design hypothesis'. IF you were able to independently from the outcome justify of why you chose that particular goal, then maybe I might agree with you that the design hypothesis is strengthened.
Comment by hrun — May 15, 2008 @ 7:04 pm
May 17th, 2008 at 4:04 pm
Sorry, hrun, I didn't ignore you, yesterday. I had almost finished typing out my reply, when time ran out at the library, and my computer went down, with all my comments. I'll try again.
Comment by Bilbo — May 17, 2008 @ 4:04 pm
May 17th, 2008 at 4:10 pm
Nothing more frustrating than losing a long comment.
In any case, don't feel compelled to answer all the points that I raised. I'm not sure we will reach a resolution on them. My main point is that I think you make unwarranted assumptions on the designer. And since apparently one goal of the designer (in your assumption) was for life to turn out the way it did, I think you get a lot of false positive indications of design.
Comment by hrun — May 17, 2008 @ 4:10 pm
May 17th, 2008 at 4:37 pm
If the first cells were intelligently designed, it's reasonable to assume that the designers were much more advanced in knowledge and skill in the area of bio-nanotechnology than we are. If they knew about pentoses, they probably also knew about hexoses, and knew which would best serve their purposes.
Oops, that first quote was really yours, and I copied it and didn't blockquote it and respond. Yes, and if they were limited in knowledge and skill, no doubt somewhere in their history they had done plenty of experiements. But that doesn't mean we would see them, just as we usually don't see the experiments of most the products we use today.
Front-loaded evolution hypothesizes that the first cells were designed with information that would unfold as the cells reproduced and were subject to the effects of Darwinian evolution. If that hypothesis is correct, and at least some present-day biotic reality was the goal (at least multi-cellularity), then Mike has to show that it was possible to incorporate the information for multi-cellularity into the original cells, without that information being lost.
I avoided the word "falsified" for the very reasons you make plain. I used the word "weaken," instead. We can always change hypotheses, and see if they better fit the evidence, and then look to see if new evidence supports or weakens the new hypothesis. The history of figuring out what Stonehenge is all about is a good example.
Reproduction is part of the hypothesis. From the articles I referred to, it looks, right now, as if ribose might be optimal for that. But I would like to see what the other pentoses would do, personally. Perhaps they're better, and Mike's hypothesis would still be weakened.
True. Mike is working on the hypothesis that the first cells were designed. Since he can't produce the designer, the next best avenue seems to be an accumulation of evidence for one. So finding out that ribose is optimal for reproduction (if it is), is only a small pebble in what would have to be a mountain of evidence, before the scientific community becomes convinced. But that is what Darwin did — slowly accumulated evidence until he had a mountain.
Yes, if there were competing sugars available, natural selection would have gone for the one that helped reproduction. Were they available? And is there evidence that nature tried different alternatives? The non-teleologists has his work cut out for him, also.
"…wanted life to unfold exactly…." Not exactly. Other evidence? Try reading Mike's book.
Out of time, again.
Comment by Bilbo — May 17, 2008 @ 4:37 pm
May 17th, 2008 at 4:57 pm
How do you know? And how do you know that there are not other sugars that might be even better? And how do you know by what CRITERIA the Front Loader chose ribose of hexose and any other material?
Again, unwarranted assumption. And, with the same assumption I could point out that evolution, not design might arrive at ribose with having 'tried out' many other materials that just did not leave a fossil record.
To what end? What goal? What was supposed to be achieved? Multicelluarity? Present day biotic reality? Sure. Pick what happens today as goal and you are bound to come to the conclusion that a prior states were designed to achieve the 'present day biotic reality'.
Yes. Mike's specific hypothesis about the Front Loader and his goals would be weakened.
Yet again: The present is chosen as the goal for the Front Loader, so every past state is indicative of 'design' in order to achieve this goal.
Really. Again? Can't you make a cogent argument that fits inside this comment box to support the notion that you are not simply taking 'present day biotic reality' as the goal for the Front Loader and thus every state preceding the present day would appear to you designed to achieve 'present day biotic reality'? I actually have to read the whole book so you can adequately answer this simple question? Very disappointing.
Comment by hrun — May 17, 2008 @ 4:57 pm
May 18th, 2008 at 4:02 pm
I don't know. But it seems like a reasonable assumption — if they knew how to make ribose, they probably knew how to make hexoses. And I don't know there aren't better sugars, hence the question mark at the beginning of this thread. And I don't know what CRITERIA they would use. But Mike's hypothesis would call for an efficient way to reproduce, and ribose seems better than hexoses. Are there better pentoses for reproduction? Let's find out.
Why?
Yes you could. I think I've said that a number of times, now, haven't I?
Well, actually, the major objection to FLE has been that whatever information was front-loaded into the original cells would be lost in the history of evolution, since it had no initial function. Until recently, showing that there are ways to actually achieve FLE was a major hurdle. Now the evidence seems to be indicating that it may not be that difficult.
This thread is about ribose and other sugars, and the question of which one would be better for design and FLE. If you want to explore the whole question of FLE, I suggest reading Mike's book. It's really very good.
Comment by Bilbo — May 18, 2008 @ 4:02 pm
May 22nd, 2008 at 5:00 pm
Hope you don't mind the intrusion, Bilbo and hrun, but as Bilbo is a fan of front loading, I guess you must then find Professor John A. Davison's ideas appealing. I'm sure if you asked him he would be happy to expand on them here.
ETA Also Professor Shapiro was a reviewer of "Darwin's Black Box". A for style, F for content, IIRIR. You might enjoy his "Planetary Dreams".
Comment by Alan Fox — May 22, 2008 @ 5:00 pm
May 23rd, 2008 at 4:27 pm
Hi Alan,
I think I skimmed something by Davison a while back. Maybe you had provided the link. It seemed very amenable to FLE. I'm curious what he thinks of ID, especially Mike Gene's variety.
Shapiro reprises some of his (and his early colleague's) ideas on what other types of life there could be besides carbonaceous in the article referred to at the top. Is his "Planetary Dreams" along the same lines?
Comment by Bilbo — May 23, 2008 @ 4:27 pm
May 24th, 2008 at 1:48 am
[quote]
Or the poor stability of RNA and the high stability of DNA.
[/quote]
This assumes that stable RNA is a good thing. It makes sense that DNA should be stable since it is a more permanent storage for information. It also makes sense for RNA to be less stable since, after copying information from DNA and coding for proteins, you would want it to break down since it is no longer needed to code for those proteins (until more RNA is later needed and then used to make copies of more DNA and code for more RNA). Imagine if RNA were stable and you had all these stable RNA strands all over the place (or if you used DNA instead), it would make it difficult to code for what you wanted when you wanted since the stable RNA that was previously used to code for something never broke down and constantly produced proteins when it wasn't necessary to do so (interfering with what needed to be coded for at the time). This is just silly.
Comment by Bettawrekonize — May 24, 2008 @ 1:48 am
May 24th, 2008 at 2:18 am
hrun
What? Proteins have a diverse array catalytic functions.
What? The function of RNA is not that of a catalyst. RNA serves a different function.
Comment by Bettawrekonize — May 24, 2008 @ 2:18 am
May 24th, 2008 at 1:14 pm
I could kinda see how it would make sense for the framework of a design (that is, the part of the design that is shared by many other designs) to be more optimal than any specific (non - shared or less shared) usage of that framework. Take these forums for instance. Like any other forums, these forums aren't perfectly structured (no pun intended). Yet, all websites share similar HTML code and are coded in the same language. We would expect far fewer flaws in the compiler used to make this website. The back end structure of this website follows a much better logic than the GUI of this website, with far fewer flaws, because the back end is common among many other websites (so if it had flaws, it would be reflected among many other websites). If I write a program in C++ using a common compiler that many other people use, it's conceivable that my program could have flaws. However, the compiler I am using would be expected to have far fewer flaws because of the fact that if it had flaws, they would likely be reflected by many others who use that compiler (not just by my program).
Comment by Bettawrekonize — May 24, 2008 @ 1:14 pm
May 27th, 2008 at 4:10 pm
Interesting comments on why we would want RNA to be unstable, Betta. That seems to support a design hypothesis. I know next to nothing about computer, so I didn't follow all that computer program stuff.
Comment by Bilbo — May 27, 2008 @ 4:10 pm
May 27th, 2008 at 4:23 pm
Yes proteins do and RNA not so much.
RNA still serves as a catalyst, for example in splicing reactions. And, looking at the ribosome, it appears to have served as a catalyst for different things in the past.
That's the whole point: It appears that RNA once served as information storage and catalytic system. It was supplanted by a 'more optimal' information storage and catalytic system (DNA and proteins).
If the inference about optimal material being an indication of design is actually valid, this information should count as countering that specific argument.
In the end, I think the whole premise of the argument is flawed, since there is no way that we can infer the goal of the design independently of what the actual outcome was. It's the typical puddle-logic: Since organisms now are optimal replicators Bilbo posits that the designers goal must have been to build optimal replicators. Since the organisms are optimized for their goal design is being inferred.
This type of logic always leads to the conclusion of design.
Here's another one: The designers goal was to shape evolution in a way that eventually self-aware beings would come about. Since self-aware beings actually came about we can infer design.
Comment by hrun — May 27, 2008 @ 4:23 pm
May 27th, 2008 at 4:33 pm
Yes, depending upon how strong the evidence is that RNA once served as an earlier information storage and catalytic system, this would count against a design hypothesis.
So this would serve as a good place to focus research. Non-teleologists looking for pathways from non-RNA to RNA to ribosomes. Teleologists looking for design hypotheses that would explain RNA's role in ribosomes.
As to the rest of your comments, hrun, we've gone down this road a few times, and I'm getting bored.
Comment by Bilbo — May 27, 2008 @ 4:33 pm
May 27th, 2008 at 4:36 pm
If there are a million roads and only one leads to an outcome that can be evidence that the outcome was goal directed or a very chancy proposition.
Comment by Bradford — May 27, 2008 @ 4:36 pm
May 27th, 2008 at 4:42 pm
By the way, hrun, are you reading Mike Gene's book, yet?
Comment by Bilbo — May 27, 2008 @ 4:42 pm
May 28th, 2008 at 12:28 am
I know. I never said that RNA can not act like a catalyst. I said that the function of RNA is not that of a catalyst. In other words, it's not their primary purpose. They serve a different function. How well do proteins do what RNA does best? Proteins and RNA both have different functions, but that's not to say that they can't do whatsoever what the other can do.
Think of it this way. A biologist may know some math, but he's not going to know math as well as a mathematician. If you want to do something that requires a deep knowledge in math and biology, you could hire a biologist and a mathematician (you could also hire someone who knows both very well, but it could be that limiting factors would make it more difficult to find someone who is well versed in both biology and math. There could be liming factors here that could make something that serves the function of RNA and the function of proteins not feasible, impractical, less efficient, or maybe even physically impossible). Sure, the biologist may know some math and the mathematician may know some biology (and what they do may overlap to some degree), but generally, the function of a mathematician is that of doing math, and the function of a biologist is that of applying biology.
I think this is mostly just speculation (not based on any empirical evidence whatsoever). Just because RNA can serve as a catalyst is not evidence for the notion that your speculated scenario is true. The fact that RNA can serve as RNA and even as a catalyst under certain circumstances seems to indicate the efficient nature of RNA.
I don't think that it "appears that RNA once served as information storage and catalytic system."
I think that it appears that RNA serves a different purpose than DNA and proteins and that's why they do different things best.
Comment by Bettawrekonize — May 28, 2008 @ 12:28 am
May 28th, 2008 at 1:04 am
The two functions appear mutually exclusive. The codon sequences of information laden mRNA for example are not those found in the catalytic version. That one RNA molecule would perform genomic and catalytic functions simultaneously is what is called for.
Comment by Bradford — May 28, 2008 @ 1:04 am
May 28th, 2008 at 1:59 am
I don't take the position that degree of optimality can be used as a very reliable indicator for or against design. Level of optimality with respect to design detection is more like a heuristic (something that tends to be true but is not necessarily true) and not an algorithm (something that is always true or always yields the correct answer). For example, I can kinda see why it makes sense for life to be more optimal (though not necessarily completely optimal) at more fundamental levels (that is, parts of the design shared by many other designs) than at less fundamental levels (parts that are shared by fewer other designs) but I don't think that we can conclude that something isn't designed just because something is not more optimal at more fundamental levels. I think the problem here is that we need to know the purpose (though we could try to infer purpose based on function, but this is another heuristic and not an algorithm) and capability of the designer.
I guess one could ask, is increased optimality at more fundamental levels with respect to function something only seen in designed objects (well, I guess a group of designed objects will be necessary if one wants to determine what levels are more fundamental, or rather, what characteristics the group shares in common) when origins are known? If the answer is yes, then I suppose that it is reasonable to conclude that optimality at more fundamental levels can reliably indicate design.
Comment by Bettawrekonize — May 28, 2008 @ 1:59 am
May 28th, 2008 at 9:13 am
Read up on self-splicing. The very molecule that carries information also carries catalytic function.
Comment by hrun — May 28, 2008 @ 9:13 am
May 28th, 2008 at 9:28 am
So what is the primary purpose of RNA then? The bulk of RNA found in cells is RNA that functions as a structural scaffold in ribosomes and tRNAs. So the function of RNA is 'scaffolding'? RNA is without a doubt a multifunctional molecule, acting as information carrier, catalyst, structural scaffold, regulator, … and who knows what else.
How can you come to that conclusion without looking at the optimality of undesigned objects?
Rain clouds optimally desalinate water and distribute it across the world. Must be design. Or can you come up with a more efficient way to do it? The ozone layer is optimally designed to protect us from UV rays. And so forth and so forth.
Everything around us is perfectly suited to support life as we know it. And one way or another, some people decide that this must have been the goal of the designer, and thus conclude design. It remains circular logic.
Yes. And this optimal efficiency should probably be also seen as indicator for design. You see, because DNA is optimal for long-term information storage, design is inferred. Because proteins are optimal for catalytic functions, design is inferred. And because RNA is not good at neither, but still does both, design is inferred. It's a win, win, win situation.
Is there any scenario you can imagine, where some aspect of a process occurring in organisms that are thriving on this planet, that do not show 'optimality' in some way or another and thus would indicate 'non-design'?
Comment by hrun — May 28, 2008 @ 9:28 am
May 28th, 2008 at 9:29 am
Which outcome would not be evidence of a goal directed process or a very chancy proposition? Are there any?
Comment by hrun — May 28, 2008 @ 9:29 am
May 28th, 2008 at 9:41 am
Like DNA.
Comment by MikeGene — May 28, 2008 @ 9:41 am
May 28th, 2008 at 10:14 am
hrun
I would say that, in most organisms, the primary function is for it to convert DNA into proteins (with the help of ribosomes).
So what? This just helps demonstrate good design. A cell phones primary purpose of to act as a cell phone, but it can act as a camera phone (though a digital camera does a better job) when it needs to, a calculator (though an independent calculator tends to do a better job), a GPS, a word processor, and many other things. The fact that the cell phone can do all that is good design. The fact that RNA can also do multiple things is also good design. With all its functions, it would make sense for a designer to choose it.
The point here is that we're looking for the emergence of such characteristics.
Well, in the case of our environment, ecosystem, ozone layer, etc… one could argue that we do not know the origins (we never observed it). The point here is that we would look at how groups of systems with more optimal frameworks (shared characteristics) emerge (more optimal than their less shared characteristics) and see if