Bio
That is an example of what I was talking about in my last post. Have you thought about how a human being could possible exist with only 20,000 genes? The answer is that 5a has been proven false. As has 5c. And I am assuming you understand the significance of the wobble base (this is very old news) so 5d is not entirely true either.
Sy,
Don’t be vague. If you are going to say that I have used an inappropriate term then post how I used it and lets us see.
If you are going to say that RNA World is falsifiable, then tell me how we would falsify something based on what we do not know? Show me someone who says the RNA World is impossible, and I’ll show you someone who will say we just don’t yet understand how it happened.
And please do not merely suggest that I have used a “law-like” statement without support, post what it is so that we can see if that is indeed the case.
And don’t suggest that I have made a claim that is out of date without having the courtesy of saying what that claim is.
I am as capable of making mistakes as anyone else, but I am fairly confident I can defend the things I’ve said, and on the core issues of semiosis during protein synthesis, I know I can.
You don’t think that the reading frame in gene expression matters?
I find it amazing that anyone would argue that the orientation of a spatial representation does not matter.
So the TAG in the sequence CC TAG CC can be CTA or AGC or GAT.
Is this the position here?
Thanks for the elucidation. Based on what you just clarified, I would rephrase your second statement as follows: “So, without these IC relationships, the [semiotics-based] system could not physically accomplish what must be done, and the [semiotics-based] living cell could not be organized. It is a dictate of physical law.” Am I understanding that correctly?
If I am, then it seems that your contention boils down to this: A semiotic-based system needs semiotics to function. That insight doesn’t strike me as especially profound or helpful…but maybe I’m missing something.
Hope you feed this feedback useful.
Grace and peace,
Chris Falter
Perhaps not. I am interested in how the system actually works. Nucleic acids do not represent amino acids. The system requires something to establish what is being represented. That is the way it is was predicted. That is the way it was found. On what grounds should we ignore that?
Now you can see why everyone is confused, Bio. I tried to offer a clarification, and your response is kind of muddy.
That’s fine, a lot of good science is built on those kinds of interests. Unfortunately, your statement about what impassions you does not help us elucidate the logical scope over which your theory operates. Does the following statement…
…apply to local dynamics-based systems? Or does it not?
A local dynamics-based (to use your terminology) RNA world may provide an alternative. As many in this thread have noted, we do not yet have the tools or data to falsify these hypotheses. At the same time, the experimental work so far shows it is plausible enough to justify continuing work on acquiring the tools and data to falsify it.
You have detected reluctance among us to jump on board your theory, Bio, and it seems you find that frustrating. The reason I’m reluctant to jump on board is that supremely intelligent, godly theologians of the church in the past have built theories that made assumptions about what the science of the time could not falsify or confirm–and then those assumptions turned out wrong. Galileo did not have the tools or data to falsify (or confirm) heliocentrism, however passionately he wrote. It was really Newton who clinched the deal for heliocentrism, over a hundred years later. In retrospect, we can see that the church’s vehement advocacy of geocentric interpretations of Scripture, and rejection of heliocentric interpretations, created much damage. So I would rather not build my case for faith in God on something so tenuous as the current inability of science to render a definitive opinion on a subject.
Of course it matters. My point was that there is not one and only one initiation site. Transcription is far more complex than that. Check out any modern text on molecular biology, Alberts or Lewin for example.
Nobody is arguing that the basic biology of translation that you are telling us about is false. We all learned this in graduate school, (in my case 4 decades ago). We are simply trying to understand how you get from those facts to your absolute statements about IC. Chris’ point is valid. A new theory of how biology works cannot be constructed from philosophical ideas of what is impossible. But I know you are not convinced, and I am done. Peace and good luck.
Tangential note: in the paradigmatic system of the kind Biosemiosis is talking about, written human text, protocols for determining start, stop and reading frame are optional. It’s quite possible to produce readable text without them, and it’s been standard practice in some writing systems. For example, here’s a page from Codex Vaticanus, showing the beginning of Hebrews. Word and sentence breaks are both generally absent.
[quote=“Sy_Garte, post:108, topic:4388”]
I am not saying that there are no effective ribozymes.[/quote]
Hello Sy,
That wasn’t my question. WHY is peptidyltransferase a ribozyme?
Does it? You just made a very testable prediction.
I think you haven’t supported your claim nor answered my question.
[quote]RNA life implies that all cellular functions (or at least the minimum required for a cell to live) be catalysed by ribozymes, which lack the chemical diversity available to proteins.
[/quote]But the point you seem to be missing is that ribozymes did not have to perform those functions very well!
Nobody knows. The theory of RNA world says it is a holdover from that world that survived to the present. But we dont know that is true.
That could be true. I have read papers that posit a very error prone world between RNA and DNA to allow for code evolution. Again that might be true. But there is a limit to error prone systems as they approach error catastrophe. Early life could likely have avoided that issue, but if ribozymes did in fact not perform their functions very well, then that is supporting the first statement I made, namely that RNA life was not very robust (if it did exist). And with high error rates, evolution becomes problematic.
I have never said that I dont believe in RNA world. Its possible. But I do think that some of the experiments used to demonstrate RNA evolution are not very convincing, especially those that use PCR to “help” the evolution along.
Chris, nothing I am doing is even slightly analogous to trying to interpret scripture, or build a theory for the church. I have the much more modest goal of promoting what is already settled science regarding the operation of the genetic translation system. No material observation I am making is even controversial. And unlike the sentiment expressed in your post, I fear absolutely nothing about the material world – particularly the demonstrated physical necessity of semiosis in the organization of the cell.
Sy,
I have enjoyed reading your posts here as a lurker. Your reassuring demeanor and even-handedness are great assets. But you clearly misunderstood the issues in the previous thread. I didn’t want to address it with you then, instead, I felt like you would just see the corrections given to the main conversation partner on that thread. I was wrong about that. And now you’ve brought that misunderstanding here. It is all very unfortunate to my mind.
Sy: The answer is that 5a has been proven false.
Bio: You don’t think that the reading frame in gene expression matters?
Sy: Of course it matters. My point was that there is not one and only one initiation site. Transcription is far more complex than that.
This is just ridiculous. You tell me that 5a is “proven false”, which is entirely mind-boggling on its own. So I simply ask if you really think it doesn’t matter, and you return with not that 5a has been “proven false” but that the most ungracious possible interpretation of my words can be attacked for rhetorical purpose – as if anyone could possibly believe that my words actually suggested that the genome has only one initiation site. Good grief.
In 1961, Crick et al were summarizing their experimental results in the paper General Nature of the Genetic Code for Proteins. Of the code, they wrote:
(a) Three bases code one amino acid. (b) The code is not of the overlapping type. (c) The sequence of the bases is read from a fixed starting point.
Look at those words. I am willing to bet that no one today (and certainly not a trained professional) has ever read those words and thought Crick was saying that the genome has only one initiation site.
As I said, I think these are fairly unfortunate statements on your part, which you may now defend, only making it even more dumbfounding.
In any case, it is a perfect snapshot of every objection I’ve received here on Biologos. Your group will fail if this is any indication of how you intend to address physical evidence. The YECs will smell a rat, and the hated IDers will hoot at you. There isn’t a person on this site that has even come close to addressing the issues raised by semiosis. Steve wants to know the physical reason behind the need for two objects instead of one, and he gets the answer in the very next post where he promptly ignores it. But the moderators step in to say it’s all just swell.
ThathastobethesingularmostridiculousattemptatobfuscatingsemiosisthatIhaveeverseen.
Hello Bio,
As we’ve discussed, these two are false.
The observations required to return a positive test result:
- A semiotic system using physical representations and protocols to translate memory into functional effects. The observable aspects of this system are characterized in the information tetrahedron model of translation.
- The use of dimensional representations to encode information into memory; where the individual arrangements in the medium are recognized in their system by their spatial orientations, which are independent of the minimum total potential energy state of the medium.
- In addition to translation protocols, the operation of the system will also require systematic protocols to establish the dimensional operation of the system itself.
Ben, equivocation doesn’t work.
i want to add that the simplest ribosyme that can replicate itself is the r18 molecule. it contain about 200 bases. so the chance for the first “gene” ever is about one in 4^200 for only one replication.
Francis Crick was a great genius, who revolutionized biological thinking. But, the fact is that we have a learned a great deal more about how cells work since his death. I am not sure you have kept up with this, which is the source of my (and other peoples) frustration. You misunderstood what I meant about alternative start sites. Here is a quote from one of many papers that discuss this. (TSS is transcription start site).
At least 6000 human genes express mRNAs with alternative first (5′ UTR) exons, and alternative TSS use is regulated in a tissue-specific manner (Carninci et al. 2006; Kimura et al. 2006; Wang et al. 2008; Yamashita et al. 2011). Recent work suggests that alternative TSS selection contributes more to mammalian mRNA isoform diversity than alternative splicing in some tissues (Pal et al. 2011). Mammalian genes with alternative 5′ UTRs tend to be lowly expressed and are more likely to encode proteins with regulatory functions than genes with invariant 5′ UTRs (Resch et al. 2009). Because the majority of alternative TSS choices do not change the mRNA’s coding potential (Kimura et al. 2006; Miura et al. 2006;Yamashita et al. 2011), any biological effects must arise from isoform-specific mRNA regulation, e.g., due to differences in translation, stability, and/or localization.
Maria F. Rojas-Duran and Wendy V. Gilbert Alternative transcription start site selection leads to large differences in translation activity in yeast. RNA. 2012 Dec; 18(12): 2299–2305.
I am sorry you feel so emotional about this issue, but I think you are over reacting. If I were to say something naive or wrong about economics (about which I know nothing) I wouldnt be that upset at being corrected. I am not suggesting you know nothing about molecular biology, you clearly know a lot. Just not enough to make broad general statements and hope to be taken seriously. I am, as I have said, sympathetic to your general idea, but not to the way you defend it.
I dont think this group has any problem in how physical evidence is addressed, and I dont understand your reaction. The typical YEC reaction that I have seen is woefully ignorant of real science (and yes, its true that real science is defined by real scientists) and as for ID, Im glad you brought that up. Maybe you should go back and take a look at the book review which was the origin of this thread.
This isn’t about emotion, Sy. An alternative start site is still a start site, is it not? The system must still establish the dimensional orientation of the script in order to produce a functional result.
yes, but your fact list is not quite right. The point is that the same gene can actually code for several different proteins depending on start sites, not to mention alternative splicing activities. I dont think you need more than the first 3 points to make your argument.
But again, (I hate to bring this up) you still need more than a post hoc hypothesis if you want to make a scientific statement. My suggestion would be to stick with a more simple philosophical argument (which in my view is as good as or superior to scientific ones) that the translation system is a symbolic representational system that is unprecedented in the universe. How it got here is beyond our current knowledge. Proving that it could not have arisen from natural chemistry (which I believe is correct) is extremely difficult.
“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6
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