The Current State of Abiogenesis Research
by chunkdz
A recent paper from the lab of Nobel Laureate Jack Szostak describes some of the best current solutions to some big problems.
Problem 1) Homochirality: Biology is universally homochiral.
Solution: Circular polarized light from interstellar molecular clouds can give amino acids an enantiomeric excess, irradiated iron ore can also tilt the balance of chirality, and grinding crystals can amplify chirality.
Problem 2) Nucleic acids don't spontaneously arise prebiotically.
Solution: Mix cyanamide and glycolaldehyde, let sit overnight, then add glyceraldehyde, incubate overnight, react with cyanoacetylene in a buffered aqueous solution of pH 6.5, then phosphorylate with urea and ammonium salts under heat, dehydrate and rearrange via intramolecular nucleophilic substitution, then cool, rehydrate and irradiate with ultraviolet light. Repeat.
There is no known way to spontaneously generate purines, but when one is found, we should be able to polymerize them on montmorillonite clay under strongly dehydrating conditions.
Problem 3) Concentration
Solution: Tide pools capture amino acids, dehydrate and condense. Freezing also condenses products between crystal grains as does adsorption on metal hydrides. Also the temperature gradients present around freshwater hydrothermal vents provide a concentration mechanism as well as a good place to make fatty acid vesicles. Which leads to the fourth problem:
Problem 4) Cellular replication
Solution: Montmorillonite clay. It catalyzes the formation of fatty acid vesicles. Using fatty acids from meteorites, the vesicles can capture self replicating RNA molecules and give them a safe place to grow. Then they can grow, capture amino acids and fatty acids from the environment, and if they grow in a solution of highly charged molecules the bubble will become a long skinny bubble, and if agitated it will break into two or more bubbles. Replication.
Problem 5) Genome replication
Solution: Fatty vesicle must be permeable, requiring the right mix of fatty acids, glycerol monoesters and
fatty alcohols, to allow raw materials to enter the protocell. Once replication is achieved, thermal cycling can seperate the newly replicated copy, perhaps in a cold pond with a local geothermal feature.
Problem 6) Emergence of complexity
Solution: Darwinian evolution and deep time.
We now have a picture of how life may have developed under prebiotic conditions. One can easily envision a scenario in which the earth was bombarded by meteorites containing amino acids, organic compounds and fatty acids which had passed through the circular polarized light of an interstellar molecular cloud, then cyanamide and glycolaldehyde were mixed in a freshwater tide pool and allowed to sit overnight, glyceraldehyde was then added and allowed to incubate overnight before reacting with cyanoacetylene in another tide pool containing a buffered aqueous solution of pH 6.5, then phosphorylated with urea and ammonium salts under heat, dehydrated and rearranged via intramolecular nucleophilic substitution before being allowed to cool and rehydrate and subsequently bathe in ultraviolet light. Once all the necessary nucleotides were present they were concentrated around freshwater thermal vents covered with montmorillonite clay and metal hydride which was occasionally exposed to the air for dehydration and concentration. Once in sufficient concentrations after a few freezing cycles and subsequent grinding, chunks of montmorillonite clay were scooped into fatty bubbles where they began to polymerize in the relative safety of their protective bubble of fat. Then when the molecules started replicating and the bubbles allowed more raw materials to permeate their fatty membranes, highly charged molecules caused the bubbles to become long and skinny which made them break and form tiny "baby" bubbles which continued to grow as long as they remained in a cold pond with a local geothermal feature nearby. Then Darwinian evolution took over and facilitated the complex machinery which we find in modern cells.
Of course, there are still a few unanswered questions.
June 9th, 2010 at 5:12 pm
I really enjoy the stuff in the Annual Reviews series of journals.
Comment by KC — June 9, 2010 @ 5:12 pm
June 9th, 2010 at 6:58 pm
Sounds like a fairly straight forward process that would be testable by experiment. When will it be tested?
Comment by Daniel Smith — June 9, 2010 @ 6:58 pm
June 9th, 2010 at 7:32 pm
Much of the scenario has been tested.
Comment by chunkdz — June 9, 2010 @ 7:32 pm
June 10th, 2010 at 12:00 am
Gee, there's just no way nature could produce fresh water of pH 6.5, drying and re-wetting pools, hot vents, hot polyphosphate-producing rocks, clay, and various small organic molecules in close proximity to each other. I mean, snow/ice near a volcanic feature with daily and seasonal variations in temperature and snow melting rates is just ludicrous. It's much more likely a divine miracle was required.
Comment by Nick Matzke — June 10, 2010 @ 12:00 am
June 10th, 2010 at 1:31 am
With all the other contaminants and the bi-chiral amino acids and sugars?
Comment by Bilbo — June 10, 2010 @ 1:31 am
June 10th, 2010 at 1:34 am
Hi Nick,
It is much more likely that software-driven biological machines were designed.
Comment by Bilbo — June 10, 2010 @ 1:34 am
June 10th, 2010 at 1:57 am
I bet things haven't changed since Shapiro wrote this in 1986.
Comment by Bilbo — June 10, 2010 @ 1:57 am
June 10th, 2010 at 2:05 am
Chain enough "natural events" in a row, Nick, and you're talking about intelligent design without realizing it.
Comment by nullasalus — June 10, 2010 @ 2:05 am
June 10th, 2010 at 6:52 am
John Sutherland's lab's long term research plan is to first work on the steps for purine synthesis, and then tie everything together in a self-driven system.
Comment by KC — June 10, 2010 @ 6:52 am
June 10th, 2010 at 7:16 am
Except there isn't any data which shows even all that would bring forth a living organism from non-living matter.
As opposed to a lucky miracle?
Comment by ID guy — June 10, 2010 @ 7:16 am
June 10th, 2010 at 7:19 am
Good for him.
He will have as much success as anyone would have trying to determine blind, undirected processes produced the Antikythera mechanism.
Comment by ID guy — June 10, 2010 @ 7:19 am
June 10th, 2010 at 7:50 am
ID Guy,
But that's not what John Sutherland's lab can hope to show anyway. What he creates will be neither blind nor undirected – how can it be, when he's expressly setting out to achieve a certain end result? There's something innately odd about talking about a researcher intending to 'tie everything together in a self-driven system'. It's almost like suggesting that creating a robot that can create a cell is a way to demonstrate that 'blind, undirected processes can create a cell'.
In the end, all such research is broadly ID research.
Comment by nullasalus — June 10, 2010 @ 7:50 am
June 10th, 2010 at 7:58 am
nullasalus,
I believe Sutherland et al., are trying to remove their interactions as much as possible.
Perhaps they can get to a point that all they need to do is set up some initial conditions.
Then we would have to determine if those conditions are plausible without agency involvement.
IOW that is how they would do it- try to remove their involvement as much as possible.
Comment by ID guy — June 10, 2010 @ 7:58 am
June 10th, 2010 at 8:20 am
ID Guy,
No doubt. It's a better system if the designer doesn't need to be there, poking and prodding every aspect of things, yes?
Front-loading, eh?
Ignoring the fact that if Sutherland was wildly successful, it would still demonstrate the ability for agents to set up and orchestrate these things.. how exactly is 'agency involvement' ruled out in the relevant way as far as ID is concerned? Denton would likely just shrug his shoulders, as would others.
After all, ID extends to cosmological scales. Rather hard to determine whether or not there's any 'agency involvement' given that open question, eh?
Sure, their involvement. But A) They can't remove their involvement completely. That would be called "Shutting the lab down and waiting to see if it happens on its own", and B) They can't remove 'agency involvement' in the relevant sense, even the ID sense.
The furthest they could get is 'Well, given these conditions, this amount of time, this set up, and these materials, this result could occur – and an agent can set these things up'. An interesting result if ever it came to pass, to be sure.
Comment by nullasalus — June 10, 2010 @ 8:20 am
June 10th, 2010 at 8:56 am
Is functional sequencing within nucleic acids addressed by any specific test(s)?
Comment by Bradford — June 10, 2010 @ 8:56 am
June 10th, 2010 at 9:58 am
[closing em]
As he did before, olegt may want to object to the implied circular reasoning.
I've pointed out "the illogic of appealing to biological evolution as the process providing the origin of those mechanisms that make biological evolution even possible". olegt seems skeptical that anyone has ever tried to take such a position, so he may want to claim that this a straw man:
Yet, a very important subset of that "complex machinery" is the complex machinery that makes Darwinian evolution work (so far as it does work). [Let's build a ladder to get out of a hole so we can go get the tools and materials needed to build ladders. e.g. here]
The trouble for olegt is that, so far as I can determine, he has nothing to put in place of such a circular claim.
Comment by eric — June 10, 2010 @ 9:58 am
June 10th, 2010 at 10:48 am
eric,
There is no circular logic here. In the summary provided by chunkdz in the opening post, Darwinian evolution is not part of abiogenesis, it takes over after self-replicating molecules arrive at the scene.
Comment by olegt — June 10, 2010 @ 10:48 am
June 10th, 2010 at 11:38 am
Is a just so story. Olegt's response to Eric that "Darwinian evolution…takes over after self-replicating molecules arrive at the scene." is more an article of faith than a demonstrable physical process.
Comment by Bradford — June 10, 2010 @ 11:38 am
June 10th, 2010 at 12:24 pm
Bradford,
I am making an argument about the plausibility of the story. I'm pointing out that eric can't even get the story straight.
Comment by olegt — June 10, 2010 @ 12:24 pm
June 10th, 2010 at 12:44 pm
pretty cool pretty neat. Some other interesting problems, the evolution of the first primitive cells. The simplest possibility would probably be just polymers with lots of negative charges interacting with molecules with lots of positive charges, and vice versa. But it’s a long way from there to life. The problem of energetic cycles,here are again many interesting possibilities, hot core and cooler oceans, reducing ocean/sea floor/land and more oxidizing atmosphere, molecules generated by incubation in space and subsequent infall to earth, reacting with terrestrial molecules, photochemistry (from a uv-rich sun), concentration gradients of a wide variety of sorts, reactions of molecules produced by energetic processes involving meteor impact/burnup. The problem of evolution of the first networks, maybe some catalytic processes had faster rates than others, and that combinations of these became self-amplifying. The principle of this kind of autoamplification is fairly straightforward; how it actually happened is not at all clear (to me, if it happened at all). The problem of the first catalysts. Maybe colloids of iron, copper, manganese, nickel etc produced in hot springs and oceanic smokers, the surfaces of acidic (or perhaps basic) minerals, acid in the water (lots of CO2 gives lots of carbonic acid in water); phosphate, sulfate, etc are also all plausible. Perhaps photoactivated sites from surface irradiation of mineral by the sun, sulfur-containing compounds produced by geological activity, heterocyclic compounds (nucleotides, imidazole) and simple carboxylic acids, metal hydroxides (e.g., ZnOH) etc tend to appear in lots of active sites in current molecular biology.
Comment by Guts — June 10, 2010 @ 12:44 pm
June 10th, 2010 at 1:04 pm
Matzke wrote:
Of course these are plausible. That's the point. I've long characterized origin of life research as a race between the 'bottom up' approach and the 'top down' approach, and that both approaches are equally valid for establishing conceptual proofs. This post is just a brief update on the race from the 'bottom up' perspective.
But since you don't seem very interested in learning what a leading researcher has to say about abiogenesis, and because you seem more interested in preaching your message of anti-creationist bigotry, perhaps your missive would be better received among your vulgar PT peers. Feel free to take your bigotted vendetta with you when you leave.
Perhaps you could treat your followers to another blog post about the dangers of Kirk Cameron? That seems more your speed. Or better yet, won't your foul mouthed minions be impressed when you blog about disgraced creationist Ted Haggard! I hear he's opening a new church in Colorado. That should start a real frenzy of poo-flinging!
Comment by chunkdz — June 10, 2010 @ 1:04 pm
June 10th, 2010 at 2:37 pm
Correction to my previous comment: I am not making an argument about the plausibility of the story.
Is the edit button ever coming back?
Comment by olegt — June 10, 2010 @ 2:37 pm
June 10th, 2010 at 2:38 pm
Yes, patience young grasshoppa.
Comment by Guts — June 10, 2010 @ 2:38 pm
June 11th, 2010 at 4:16 am
Hi Chunk,
So did you ban Nick from your thread?
Comment by Bilbo — June 11, 2010 @ 4:16 am
June 11th, 2010 at 6:04 am
The Circular Logic of Evolving the Tools Needed to Evolve
The circularity is hidden under a veil of equivocation between what Darwinian evolution needs and the "self-replicating molecules" hypothetically provided by RNA replication.
Darwinian evolution relies upon reproduction of an organism, which is a team sport with regard to the genetic information. Everything in the genome of a "winning" organism gets reproduced, just as all players on a winning team advance in the playoffs — even those players that just sat on the bench.
Even supposing an RNA World were to exist, that only would provide replication of individual strands of RNA. That is an individual sport. Only the individual strands that are replicated advance in the competition for resources. You cannot increase what you do not replicate.
RNA World replication cannot replicate complex machinery — just isolated free strands. Consequently, it cannot evolve complex machinery. It doesn't give the reproduction Darwinian evolution needs or provide the pathway to making the complex machinery needed for that reproduction.
What is worse, the strands most likely to be replicated in the RNA World are those most available for replication, i.e. those that avoid any complex interactions that would inhibit RNA World replication. In other words, selection in that context heads away from complex machinery, not toward it.
Comment by eric — June 11, 2010 @ 6:04 am
June 11th, 2010 at 7:08 am
olegt, could you please clarify this point about your definitions?
Some of your statements seem to imply that scientific progress invariably means attributing the origin of everything to law+chance. Yet, I doubt you actually intend to assert that claim. Would you agree that the advance of science in no way implies or requires that the origin of life is due to law+chance?
Comment by eric — June 11, 2010 @ 7:08 am
June 11th, 2010 at 12:50 pm
No.
Comment by chunkdz — June 11, 2010 @ 12:50 pm
June 11th, 2010 at 2:14 pm
I've noticed over the years that Nick has a hit and run posting style. He'll stop by once and a while and post a flurry of comments and then stay away for a month or two.
Comment by Bradford — June 11, 2010 @ 2:14 pm
June 11th, 2010 at 5:52 pm
fart & dart…
Comment by ID guy — June 11, 2010 @ 5:52 pm
June 11th, 2010 at 7:29 pm
This is a common missive amongst the atheist clan. They talk as if, given enough time and data, all their beliefs will be vindicated. It's as if, to them, science can only go a certain way. It's funny, in a way, because their hopes and dreams rely on one of the most notoriously unreliable forms of knowledge we know of. The reality is that science could, given enough time and data, completely crush all their hopes and dreams with results that contradict all of their beliefs.
Oh well. I think Jesus mentioned something about houses built on shifting sand…
Comment by Daniel Smith — June 11, 2010 @ 7:29 pm
June 12th, 2010 at 1:35 pm
Actually, I was impressed by how mild these reaction conditions are — unlike some previous "prebiotic" syntheses. I was just reacting to the presumption that all kinds of experimenter interference is necessary to bring these elements together, when in fact it's pretty much ice + hot rocks of the right types.
As for the origin of the ability to have natural selection, it's actually not true that you need fully capable replication before you can have natural selection:
Prevolutionary dynamics and the origin of evolution — PNAS
by MA Nowak – 2008
http://www.pnas.org/content/10...
Finally, some here have argued that the only experiment that would be valid would be if the experimenters left the lab and did nothing. This is a ridiculous and wildly unfair, and fundamentally unscientific, viewpoint to have on OOL research. If you have this viewpoint you are so far from being reasonable you have no basis on which to participate in a reasoned discussion on OOL.
For starters: (a) all chemistry experiments are controlled, if they aren't, you won't know what happened, and much of the point is to understand which reactions happen, and how, under which conditions. (b) Any vaguely reasonable prebiotic experiment has to do some very obvious things, like exclude oxygen (which was not present at 21% levels 4 billion years ago), but even this minimal, and scientifically required, "intervention", is judged inappropriate by the bizarre "no human influence on experiments" rule. (c) It is perfectly scientific to figure out under what reaction conditions a particular reaction occurs, and then survey the likely-available environments to see what might occur. On a world with lots of ice and lots of volcanos, there would be many opportunities for places with conditions like the ones discussed above. It doesn't matter if those conditions are discovered even by completely pre-planned, foresight-enabled research-inferring labwork, if it turns out that those conditions appear naturally. Newton figuring out how orbits worked does not mean intelligent intervention is needed to keep the moon, asteroids, etc. in orbit. This is no different than numerous other fields that do labwork but interpret it within the bigger picture of geology, biogeochemistry, etc.
Comment by nickmatzke — June 12, 2010 @ 1:35 pm
June 12th, 2010 at 2:12 pm
nickmatzke, you seem to prefer to cherry pick the easiest aspects (ice and hot rocks? check; "it's pretty much ice + hot rocks of the right types") and avoid the genuinely problematic issues.
Does anyone — even the OOL researchers — really believe it comes down to ice, hot rocks, and some other little details we need to work out?
Regarding inappropriate intervention, it is a simple matter to draw attention to the fact that experiments must be designed, while failing to deal at all with issues of genuinely inappropriate "help". Shapiro is no friend to ID. But the metabolism-first community has been clear that the level of helpful intervention required to get results have been inappropriate and therefore not persuasive.
Except that the issue was not whether you could have natural selection. So, you appear to have missed the point and have endeavored to answer a question that wasn't in question.
The issue is the origin of complex molecular machinery. The problem is not that there is no selection. The problem is that the selection that would indeed exist in an RNA World would push in favor of replicating strands that tend to be available for replication, and against replicating strands that have formed attachments and/or secondary structures that inhibit or discourage replication.
Consequently, selection becomes the problem not the solution. Selection doesn't favor building complex machinery because RNA replication does not replicate complex molecular machines.
Comment by eric — June 12, 2010 @ 2:12 pm
June 12th, 2010 at 3:09 pm
Eric, we have all kinds of examples of selection on replicators leading to more complexity. So your argument isn't really an argument, it's just an assertion contradicted by known facts.
My point is that many have the idea in there heads that if life had natural origins, it must have worked like this:
model1: prebiotic chemistry –> complex replication machinery originates purely by blind luck without any help from natural selection –> natural selection & evolution of the rest of life
…whereas, what scientists actually think is more like:
model2: prebiotic chemistry –> simple pseudoreplication without any complex machinery –> natural selection –> increasingly complex and accurate replication machinery, aided by natural selection the whole way –> evolution of the rest of life
…so, complaining about how #1 doesn't work — which is 90% of ID argumentation on the OOL topic and on this blog — is like, I dunno, arguing against Christianity on the grounds that Jesus wasn't a Jew. It's totally off-point.
Comment by Nick Matzke — June 12, 2010 @ 3:09 pm
June 12th, 2010 at 3:33 pm
Thanks for making that explicit. Let's look closely at the relevant steps (emphasis added).
2. simple pseudoreplication without any complex machinery
3. natural selection
4. increasingly complex and accurate replication machinery, aided by natural selection the whole way
So, somewhere between step 2 without any complex machinery and step 4 where we have increasingly complex and accurate replication machinery, we have the appearance of complex machinery. How?
The only step in between is "natural selection". Selection cannot favor something that cannot be replicated. RNA World replication cannot replicate a complex machine. So you have not solved the problem.
That word play dodge doesn't work. What is needed is not just vaguely "more complexity". (The sequence in a single strand might be considered more or less complex, but that isn't sufficient.)
The wall you have not crossed is the ability to replicate a complex molecular machine consisting of more than isolated strands (without circularly assuming you already have the help of existing complex molecular machines).
RNA replication works by forming the reverse complementary strand of a single RNA strand, which must have its bases free to form bonds with the complementary bases on the new strand. (Applying the same process to the reverse complement gives you back a copy of the original, i.e. the negative of a negative).
That process does not replicate a complex molecular machine — only single polynucleotide strands. Consequently, selection points away from complex molecular attachments.
So adding "natural selection" as a step creates the problem rather than solving it. How do those supposedly increasingly complex replication machines first develop from a process that cannot replicate them (and without making circular appeals to other molecular machinery)?
Comment by eric — June 12, 2010 @ 3:33 pm
June 12th, 2010 at 6:14 pm
Can you link to those (ahem) examples, please?
No- the experiment is valid regardless of any intervention.
My point is that if intervention is absolutely required it throws a huge wrench into the position of "blind, undirected chemical processes".
Comment by ID guy — June 12, 2010 @ 6:14 pm
June 12th, 2010 at 7:02 pm
Technically not true. There can intermediate stages between nonreplication and full replication, and natural selection acts nonetheless. That was why I helpfully posted the Nowak paper, which you unfortunately completely ignored
.
RNA can act as an information-carrier and as an enzyme ("machinery") — and does so today in many core cellular functions. These and many other lines of evidence are support for the RNA world being at least a major stage in the origin of life (whether or not RNA was the very first pseudoreplicator).
http://ncse.com/creationism/le...
http://www.ncbi.nlm.nih.gov/pu...
http://evolution.berkeley.edu/...
http://www.sciohost.org/ncse/k...
…etc…
Also, TT authorities like Mike Gene would agree that NS acting on replicators can increase complexity, so it's not just us wicked "Darwinists" who think this…
Comment by Nick Matzke — June 12, 2010 @ 7:02 pm
June 12th, 2010 at 8:33 pm
Can you link to those (ahem) examples, please?
Very unimpressive.
How are you using the word "complexity"?
Anything about functional protein machinery "evolving" via selection?
Comment by ID guy — June 12, 2010 @ 8:33 pm
June 12th, 2010 at 8:39 pm
Nick,
With the alleged evolution of the mammalian middle ear, how do you propose to test that scenario?
The same for the alleged evolution of the immune system.
And how can we differentiate between Common Descent, common design and convergence?
Comment by ID guy — June 12, 2010 @ 8:39 pm
June 12th, 2010 at 10:08 pm
Matzke:
It is amazingly simple isn't it? Rocks+ice+heat+time = Mozart.
Comment by chunkdz — June 12, 2010 @ 10:08 pm
June 13th, 2010 at 1:29 am
Wow. Well, all I can do is provide the links, I can't make you read them. Testing & the complex of the systems is discussed in each…e.g., how do you think scientists knew to look for a wild transposon related to the immune system RAG system, except because of the hypothesis that the RAG system evolved from a transposon? It was a hell of a prediction, and it was verified, and it was all laid out with complete references in the link I provided, and you totally ignored it. Oh well.
Comment by nickmatzke — June 13, 2010 @ 1:29 am
June 13th, 2010 at 1:29 am
the complex –> the complexity
Comment by nickmatzke — June 13, 2010 @ 1:29 am
June 13th, 2010 at 1:31 am
Mozart was way more complex than the the first replicators, which is what we were talking about…
Comment by nickmatzke — June 13, 2010 @ 1:31 am
June 13th, 2010 at 2:03 am
Indeed. We were talking about the primordial seeds of Mozart.
The seeds of sublime metaphysical bliss- sent from heavenly clouds light years away, sown in montmorillonite clay, and nurtured in fire and ice until it composed it's own majestic Requiem in D minor.
But I digress. Tell us, Nick, has Kirk Cameron been threatening science lately? Someone should really do something about him, don't you think?
Comment by chunkdz — June 13, 2010 @ 2:03 am
June 13th, 2010 at 9:35 am
You seem to prefer to dwell upon uncontested points, rather than the actual issue being raised or the actual positions that others take. You introduced the Nowak paper stating,
But my position has never been to deny the reality of natural selection. As I've said repeatedly, the reality of natural selection is part of the problem, not the solution, due to what it would favor (vs. could not favor) in the RNA World.
You are trying to refute a straw man (which is certainly easier than coming up with a way to replicate a multi-molecular structure in the RNA World).
More word play evasion and dodging. The issue is the origin of the complex multi-molecular machinery of cells. A ribozyme is not a multi-molecular machine. The problem that has been raised is how you get from hypothetical ribozymes and the RNA World to the complex multi-molecular structures cells depend upon.
[Side pont: You failed to attribute "Can you link to those (ahem) examples, please?" to ID guy.]
Nevertheless, for your supporting evidence you seem to want to freely appeal to selection acting on biological reproduction in order to support your claim for the capabilities of selection acting on RNA World replication.
This is once again entering into circular reasoning. It supposes without distinction that selection acting on RNA World replication has the same capabilities that may exist for biological evolution, which depends on reproduction (not replication) and the existence of complex multi-molecular machinery.
But reproduction and replication are not the same (e.g. see team sport vs. individual sport). They don't provide the same opportunities and abilities, and they cannot be treated interchangeably without entering into circular reasoning and equivocation concerning "selection".
To attempt to appeal to evidence from Darwinian/biological evolution is equivalent to appealing to evidence of the effectiveness of a ladder that one does not have as proof of one's ability to reach the ladder one does not have.
You have not escaped the circular logic supporting the origin of multi-molecular machinery.
Comment by eric — June 13, 2010 @ 9:35 am
June 13th, 2010 at 9:49 am
I read the links- they are old stories.
So you cannot tell Common Descent from common design from convergence.
Got it.
And seeing that no one knows what genes are involved for the development of the mammalian middle ear there isn't any way to test the premise that parts of the reptilian jaw "evolved" into it.
As for transposons- well there isn't any evidence they are the result of blind, undirected chemical processes.
Geez they carry with them the coding for the enzymes required to cut and paste them.
Comment by ID guy — June 13, 2010 @ 9:49 am
June 13th, 2010 at 11:13 am
"Common design" is nothing more than "I think God made it that way just 'cause, therefore I can blow off the highly successful, well-tested explanation of common ancestry."
Did common design lead anyone to look for a wild transposon related to the RAG system? No, it was the evolutionary hypothesis that RAG evolved from a transposon. It's a classic case of a hypothesis leading to a prediction of something that would otherwise be wholly unexpected, and passing that test.
This is just wrong. Any ribozyme involving more than one RNA molecule is a multi-molecular machine. And there are many such cases; plus, RNA world people seem to think it has been like this since the beginning, i.e. the earliest functional RNAs were probably cooperating short RNA molecules, which is much easier to achieve than one long strand…
Comment by nickmatzke — June 13, 2010 @ 11:13 am
June 13th, 2010 at 11:40 am
That is incorrect.
1- Common ancestry isn't well tested- it can't be tested. And how successful can it be seeing we cannot test it?
2- Common design stems from our observations and experiences with the way we design things- no need to keep re-inventing things that are already in use.
Did the premise of blind, undirected processes lead to the discovery? No.
It wasn't a blind, undirected chemical process hypothesis, that's for sure.
Comment by ID guy — June 13, 2010 @ 11:40 am
June 13th, 2010 at 11:42 am
Any evidence that blind, undirected chemical processes can produce such a ribozyme?
Comment by ID guy — June 13, 2010 @ 11:42 am
June 13th, 2010 at 3:36 pm
.. and much, much easier to justify than a single multi-molecular machine — such as the many that the cell depends upon, which you and abiogenesis stories still appear quite unable to account for. Hence the repeated need to draw attention elsewhere to points not being questioned, rather than to stay on topic.
[In passing, I will note that the idea that the cooperation of independent RNA molecules in a prebiotic, non-programmed, non-cellular environment is going to be easily achieved may not be nearly as sound or as broadly applicable as some might hope. For many functions, Meyer points out that the timing aspects do not readily make multiple enzymes an effective substitute for a single protein enzyme. But let that pass for now. That is not the question at hand. For the present discussion, we are assuming for free an RNA World with many independent strands of RNA.]
Big Hint: The question at hand is this.
"How do you account for the origin of the cell's complex molecular machines that are composed of multiple joined molecules, without making circular appeals to the abilities of biological evolution based on biological reproduction and without losing sight of the fact that RNA replication cannot replicate such a multi-molecular structure?"
Comment by eric — June 13, 2010 @ 3:36 pm
June 13th, 2010 at 4:34 pm
Actually, that pretty much is the hypothesis — a RAG transposon jumped into an immune system receptor protein gene (like they jump into thousands of other places in our genomes, more or less "randomly", although their survival isn't random, due to natural selection), creating the ancestor of the rearranging receptors we have in our adaptive immune systems today. Your ability to be immunized by vaccines depends on this lucky event hundreds of millions of years ago.
Comment by Nick Matzke — June 13, 2010 @ 4:34 pm
June 13th, 2010 at 4:39 pm
Experimental evolution has produced all kinds of ribozymes. This isn't the hard part. The hard part is getting something replicating in the first place. I thought that's what we were talking about, but now there is this bizarre argument about how multi-component systems can't evolve even once you have replicators. But this is just a rehash of the Behe/IC debate which has been had a million times, and even various TT regulars like Mike Gene have conceded that IC isn't actually a strong block to the origin of a complex system through natural evolutionary processes.
Comment by Nick Matzke — June 13, 2010 @ 4:39 pm
June 13th, 2010 at 6:33 pm
Did the premise of blind, undirected processes lead to the discovery? No.
That blind, undirected chemical processes can produce transposons?
1- Whatever survives survives. Natural selection is nothing more than a post hoc/ ad hoc narrative.
2- Transposons have in their coding the code for the enzymes required so they can "jump". Just because we don't understand them doesn't mean they are random by any means.
As far as we know they are as "random" as a computer program's "go to" statements.
Any evidence that blind, undirected chemical processes can produce such a ribozyme?
That doesn't answer the question.
I am sure we can produce ribozymes.
But do they just form, spontaneously?
I know that.
And I also know that living organisms are much more than replicators.
Also IC- depending on the number of core components- is a huge roadblock to blind, undirected processes.
There just isn't any evidence that genetic mistakes can build anything from scratch.
Comment by ID guy — June 13, 2010 @ 6:33 pm
June 13th, 2010 at 8:22 pm
ID guy is right to find this unpersuasive. Scientists can artificially control iterative rounds of selection and replication with variation to discover sequences that exhibit any property they intend to select for. It is not much different in this respect from artificial breeding for the breeder's preferences.
A weak point is that the breeder's intention need not have any necessary correspondence to what would be selected and promoted in an undirected wild situation. The artificial "breeding" could, for example, choose to force replication (with variations) of a sequence's tendency to bind to some molecule, despite the fact that such a property in the wild could make the particular strand unavailable for replication and therefore less likely to be replicated rather than more likely. Nevertheless, this does not in any way deter the breeder's ability to direct the evolution to discover and enhance the chosen desired characteristic.
Stating the obvious: that is not an example of an undirected process.
First, we have been talking about complex molecular machinery composed of multiple molecules, not vaguely about "multi-component systems" — an ambiguous phrase ready made for equivocation.
We are also not just vaguely wondering whether they can "evolve", i.e. change once they exist, but rather specifically about their origin, i.e. how such functional structures could arise and proliferate before biological reproduction is available.
Regarding "…this bizarre argument…", what would be bizarre is for someone to think that abiogenesis has no need or responsibility to account for the origin of such structures, which all cells depend upon. This omission would be doubly bizarre once we notice that the RNA World cannot replicate such a structure. It would also be bizarre, as well as logically circular, to imagine that evidence taken from biological reproduction and evolution shows what RNA World replication can do.
Your feigned surprise is also quite bizarre and incredible. Have you been reading the posts you've been responding to? Here is part of one of mine from two days ago, which clearly and repeatedly assumed replication and examined the subsequent limitations (as have my posts since then):
Already then it was plain, and likewise ever since. The question is about the inability of RNA World replication to account for the origin and proliferation of functional multi-molecular structures as distinct from "individual strands of RNA".
Nope. This is about abiogenesis, not about what can or cannot happen through the natural processes of biological evolution.
The fact that you equate this to discussions about biological evolution shows that you are still leaning upon circular reasoning in order to dismiss it as "just a rehash". Your logic implies that we could assume that RNA World replication is not any different from biological reproduction and has all the same capabilities and properties.
In short, you are clearly still arguing as if biological evolution is effectively available to abiogenesis to help produce the multi-molecular structures needed by biological evolution. You are still trapped in circular logic.
Comment by eric — June 13, 2010 @ 8:22 pm
June 13th, 2010 at 8:31 pm
olegt, would you still to try to tell me that no one would actually argue as though abiogenesis can be supported by appealing to the capabilities of biological evolution?
At times you seemed to think this was a straw man attack, since no one would do such a thing. And yet, time and time again, it seems Nick cannot go more than a few posts without appealing to biological evolution for support.
Comment by eric — June 13, 2010 @ 8:31 pm
June 14th, 2010 at 12:27 am
eric,
I find nothing objectionable in it. Evolution is descent with modification, so self-replicating entities that respond to selective pressure evolve by definition.
From Science Daily in January of 2009:
How Did Life Begin? RNA That Replicates Itself Indefinitely Developed For First Time.
Comment by olegt — June 14, 2010 @ 12:27 am
June 14th, 2010 at 7:15 am
olegt,
So implicitly, since you now "find nothing objectionable in it", it seems you are no longer claiming it is a straw man attack for me to point out that it happens, i.e. that some "argue as though abiogenesis can be supported by appealing to the capabilities of biological evolution" — even though earlier you wrote:
That was in response to me making the very same argument that I am making currently concerning the illogical circular reasoning of appealing to biological evolution. I've even kept the same ladder metaphor.
However, the issue has never been that the RNA World would not "respond to selective pressure" or that sequences could not change.
[Indeed, your own cited article (the one that claims "RNA That Replicates Itself Indefinitely" for a process that lasts only as long as the supply of half-enzymes sequenced and supplied by the scientists) also shows that scientists can direct change using "a method of forced adaptation" to reach a "goal". "Ultimately, this process enabled the team to isolate" an improved enzyme that "fulfilled the primary goal" the team had chosen from the start. I agree that this directed artificial selection process does work, just as artificial breeding works. Of course, stating the obvious again, what those scientists did was not an example of an undirected process.]
On the contrary, I have consistently insisted there would be natural selective pressure — albeit not in the direction the abiogenesis story needs to assume it will go, i.e. not toward making multi-molecular machines.
The issue of illogical circularity is the illegitimacy of vaguely supposing that biological reproduction and prebiotic replication are effectively the same thing, though they are not, or that evidence for the power and effects and outcomes and capabilities of biological evolution can be used interchangeably as evidence for what the RNA World would do, as Nick has been doing repeatedly now.
Are you still sure you "find nothing objectionable in it"? Does this mean you endorse and support the practice of citing biological evolution and then treating abiogenesis as "just a rehash", i.e. as though abiogenesis can be assumed to be able to do everything biological evolution can do and there are no significant differences worth serious attention? Is that really a position you now want to defend and stand by?
Comment by eric — June 14, 2010 @ 7:15 am
June 14th, 2010 at 7:21 am
Not self-replication oleg:
It takes two- one to act as a template and one to catalyze one measly bond.
IOW not only were the required template and catalyst synthesized so were all the RNAs tha were then joined together by catalysizing that one bond.
biologic institute responds to the RNA replication experiment.
Comment by ID guy — June 14, 2010 @ 7:21 am
June 14th, 2010 at 7:44 am
LOL — what a stunning breakthrough!
Comment by eric — June 14, 2010 @ 7:44 am
June 14th, 2010 at 8:25 am
eric,
Remember: you've been trying to establish circularity of logic in OOL theories. So far it hasn't worked. You would be right if researchers claimed that abiogenesis follows from Darwinian evolution (and nothing else). That is certainly not the case. Darwinian evolution begins after self-replication. It does not precede abiogenesis.
Back to the drawing board.
Comment by olegt — June 14, 2010 @ 8:25 am
June 14th, 2010 at 8:31 am
Biologic Institute seems to be much better at blogging than at doing biological research. No wonder: their research equipment consists of one freezer and two Apple computers.
Comment by olegt — June 14, 2010 @ 8:31 am
June 14th, 2010 at 8:37 am
And what do you base that on?
Or are you just upset that your example was shot down by reality?
Yes we understand it starts with that which needs explaining in the first place.
Comment by ID guy — June 14, 2010 @ 8:37 am
June 14th, 2010 at 8:40 am
What's their record of publications, Joe?
Comment by olegt — June 14, 2010 @ 8:40 am
June 14th, 2010 at 8:42 am
olegt: "Darwinian evolution begins after self-replication."
No, Darwinian evolution (a.k.a. biological evolution) begins after we have living cells that can reproduce. That was explicit from the very beginning with the Origin of Species. Darwin assumes living organisms in one or a few forms as a starting point. He describes the Origin of Species, not the Origin of Life.
The question I posed to you, which you are so far avoiding, is this:
So, are you really wanting to treat RNA World replication as though it is the same thing as biological evolution? Do you really defend treating Darwininian/biological evolution and the evolution of the RNA World as synonyms?
In other words, do you really think this is sound logic:
Can the RNA World do this?
Well, here is evidence that shows biological evolution can do this.
OK, well that proves it.
Comment by eric — June 14, 2010 @ 8:42 am
June 14th, 2010 at 8:56 am
dick,
What is the publication record pertaining to blind, undirected chemical processes?
IOW get your house in order. Your negative attacks on ID are not positive evidence for your position.
Comment by ID guy — June 14, 2010 @ 8:56 am
June 14th, 2010 at 9:00 am
p.s. to olegt,
…and if you really do want to claim there are "no significant differences worth serious attention" between biological reproduction and RNA World replication worth serious attention, then please provide your description of how the RNA World evolution creates and proliferates multi-molecular machines — even though RNA World replication cannot replicate a multi-molecular machine.
Actually, whatever position you decide to take, I'd like to hear your explanation of how that is a reasonable expectation. Thanks in advance.
Comment by eric — June 14, 2010 @ 9:00 am
June 14th, 2010 at 9:01 am
And BTW lack of publication does not mean lack of research.
Comment by ID guy — June 14, 2010 @ 9:01 am
June 14th, 2010 at 9:27 am
eric wrote:
Not to split semantic hairs, eric, but Darwinian does not exactly mean as set in stone by Charles Darwin. Try to argue in a similar way about Newtonian mechanics and you'll see what I mean. For one thing, Darwin did not know about the existence of RNA back then. But whatever Darwin thought was Darwinian evolution, the current understanding is a bit different. The concept is now applied in a wider context.
For example, viruses do not have cells, but that does not preclude biologists from coming up with titles like Positive Darwinian evolution in human influenza A viruses. In fact, there is no agreement on whether or not viruses are alive. There is no question, however, that they evolve and do so along the lines of Darwinian evolution.
Comment by olegt — June 14, 2010 @ 9:27 am
June 14th, 2010 at 9:34 am
True had Darwin knew what we now know he wouldn't have proposed his "theory".
Actually there is a question about that- Darwinian evolution requires the processes to to blind and undirected.
And there just ain't any evidence to support that claim.
Comment by ID guy — June 14, 2010 @ 9:34 am
June 14th, 2010 at 9:38 am
That was funny Olegt. After making a good point about Newtonian mechanics you revert to the phrase Darwinian evolution instead of simply evolution. In the context of OOL evolution or continuous change is not an apt descriptor of the problem. We know where the change must have been directed i.e. to an initial cell. It is within that perspective that a self-replication process must be assessed. Change toward a specific outcome is needed to be shown. That outcome is a given.
Comment by Bradford — June 14, 2010 @ 9:38 am
June 14th, 2010 at 9:43 am
Bradford,
Nothing funny about that. Evolution in this context does not simply mean continuous change, it is something more specific, namely descent with modification.
Comment by olegt — June 14, 2010 @ 9:43 am
June 14th, 2010 at 9:52 am
Descent with modification- another vague claim.
Geez baraminology accepts decent with modification…
Comment by ID guy — June 14, 2010 @ 9:52 am
June 14th, 2010 at 12:21 pm
OK. What data assures you that modified molecular RNA descendants ever more approximate a self-replicating cell?
Comment by Bradford — June 14, 2010 @ 12:21 pm
June 14th, 2010 at 12:37 pm
I did not make that claim, Bradford. Origin of life is work in progress.
Comment by olegt — June 14, 2010 @ 12:37 pm
June 14th, 2010 at 3:18 pm
IOW someone is working on a catchy and elegant narrative…
Comment by ID guy — June 14, 2010 @ 3:18 pm
June 14th, 2010 at 10:10 pm
Would it be correct to take that as an indication that you don't have an explanation about how multi-molecular machines evolve from an RNA World?
Also, would you agree that the advance of science in no way implies or requires that the origin of the biological life we see is due to law+chance? Your definitions don't equate progress with vindication of abiogenesis, do they? (cf. early question here)
Thanks in advance for your clarification regarding your definitions.
I don't want to get bogged down in semantic hair splitting, especially when the critical question doesn't change either way one says the words.
Either way, the question I'm posing to you concerning the use of "evolution" is this. Do you really find nothing objectionable about using evidence for what evolution from cellular reproduction is able to do to support claims about what RNA World replication will do? Do you really see no significant difference between these, such that they are synonymous, "evolution" is just one thing, and evidence for the former is perfectly acceptable as evidence that applies to the latter? Everything that can happen through cellular reproduction will also happen through RNA replication?
If that isn't your position (and I would hope it is not), please clarify where you do stand about propping up claims about replication with appeals to evidence from reproductive biological evolution.
Comment by eric — June 14, 2010 @ 10:10 pm
June 16th, 2010 at 11:45 pm
A Handy Reference to Typical Failed Dodges for the Origin of the Cell's Multi-Molecular Machines
(suitable for easy future reference)
The Problem:Cells depend upon many complex multi-molecular machines. If abiogenesis is true, what undirected process could account for the origin and proliferation of multi-molecular machines? An RNA World clearly could not make use of such machinery, or the cell's coordinating programming for such machines, to help create the first instances of such machines. This problem is compounded by the fact that, although the RNA World could replicate individual RNA strands, that kind of replication cannot replicate multi-molecular structures.
Some Typical Ways to Not Deal with the Problem:
1. Redirect Attention Elsewhere (e.g. by changing words, definitions, the focus of the topic, etc.)
Stage magicians everywhere know the importance of redirecting the audience's attention away from what you don't want them to notice. Examples:
a) "As for the origin of the ability to have natural selection, …" (except that isn't the problem)
b) "…we have all kinds of examples of selection on replicators leading to more complexity…" (except getting just "more complexity" of any kind isn't the problem either)
c) "RNA can act as an information-carrier and as an enzyme ("machinery")…" (as if defining machinery to be just a single strand makes the problem disappear? Not.)
d) "…the earliest functional RNAs were probably cooperating short RNA molecules, which is much easier to achieve than one long strand…" (So if there can be multiple independent strands, does that make the problem of functional multi-molecular structures disappear? Off target yet again. [Plus the use of "cooperating" is gratuitous, since the molecules have no intention of cooperation and no guiding programming and control such as exists in a cell.]
e) "The hard part is getting something replicating in the first place. I thought that's what we were talking about, …" (Never was the issue being raised.)
f) "…now there is this bizarre argument about how multi-component systems can't evolve even once you have replicators…" (Yet another false characterization of the problem.)
2. Vaguely Invoke Natural Selection as a Blank Check Without Considering Specifics
"Natural selection" often serves as a power word that is assumed, without need of scrutiny or evaluation, to provide whatever might be needed in any setting, much like a magic wand or wishing ring. This serves well to fill in any troublesome gap. Example (emph. added):
However, as Allen MacNeill has correctly observed (emph. added):
When we actually consider the influence of natural selection in the RNA World environment, the requirements of replication push toward increasing the frequency of those RNA sequences that avoid any complex secondary structure (e.g. psuedoknots, etc.) and/or attachments to other molecules that would prevent or inhibit their availability for replication.
In short, critical examination indicates that RNA World natural selection would favor moving away from complex multi-molecular structures rather than toward them. The sequence variations that are more likely to enter into such configurations can thereby become less likely to be replicated.
3. Point Instead to the Directed Process of Artificial Selection and Goal-Driven Evolution as Evidence
We know selective breeding can be used to force biological change toward the predetermined goals of the breeder. The same is true at the molecular level, but it is not an undirected process and it doesn't reveal what would happen due to undirected change. Furthermore, even directed artificial selection cannot enable RNA World replication to replicate a multi-molecular machine. It is irrelevant to solving the problem.
See comments on "Experimental evolution has produced all kinds of ribozymes."
For a look at a particularly vivid example, see the comments here regarding the article proclaiming "RNA That Replicates Itself Indefinitely" and their use of "forced adaptation" to reach a "goal".
4. Point Instead to Biological Evolution as Evidence (often while making vague references to "evolution" or "natural selection")
The vague references are important because they enable the fallacy of equivocation, wherein different things are treated without distinction as though they were the same thing.
Biological evolution with biological selection depends directly upon biological reproduction, which is fundamentally different from the strand replication of the RNA World.
a) Reproduction duplicates information from the entire genome, even including duplicated genes that may have lost their former function. (These are considered to be important to biological evolution.) Thus, it is like a team sport. A reproductive "win" advances the whole team, even the bench sitters. Replication is an individual sport. In the competition for resources, strands are copied (or not) on an individual basis, and this affects the results (cf. item #2 above).
b) Reproduction depends upon the fact that cells already have complex multi-molecular machinery. Replication does not.
c) Reproduction has no problem duplicating the ability to create complex multi-molecular machinery, and variations may revise that machinery in the process. Replication cannot replicate multi-molecular structures at all.
It is broken, circular reasoning to invoke evidence from biological reproduction as though it tells us what the RNA World could do to create the first multi-molecular machines using only replication. It is exactly like supposing that one can use the help of a ladder one cannot yet reach in order to reach that very ladder that one does not yet have.
Examples of using reproduction based evidence:
Using examples from biological evolution to defend increased complexity through natural selection, e.g. specific example here from the earlier list here.
Pointing to claims that biological evolution might be able to create Irreducibly Complex structures.
5. Point Vaguely to Expectations that Science Will Progress, and that this is a Work in Progress
Although true, such observations are irrelevant to the problem because they tell us nothing about whether there is an undirected process that would create the cell's multi-molecular machines. To imply that the progress of science can be equated with vindication for this particular leap of faith would be an example of the fallacy of begging the question, i.e. assuming the truth of the very point that is in question and that needs to be shown.
Everyone knows that science advances, but that doesn't tell us which stories will be vindicated and which will need to be discarded because they didn't hold up. The reality may be that intelligent direction is required to create the cell's complex multi-molecular machinery.
6. Give the impression that the problem is essentially already solved, and not worthy of time or attention.
This is a version of "Nothing to see here. Just move along."
Example: "… this is just a rehash of the Behe/IC debate which has been had a million times, …"
As a retrospective variation on this, if the topic comes up again, one should not be surprised to hear some version of, "We've already covered all that.", without any acknowledgment of the fact that there was no solution to the problem.
7. The Disappearing Defender
If all else fails and the problem can't be made to disappear, then one can disappear from the conversation without dealing with the problem, typically without even acknowledging that any serious problem exists.
Comment by eric — June 16, 2010 @ 11:45 pm
June 17th, 2010 at 10:07 am
eric,
You seem to not have addressed the issue we were discussing, namely that Darwinian evolution is not restricted to cellular organisms. A classic example I have provided is the evolution of viruses, which have no cells, yet we apply the principles of Darwinian evolution to them. So the restriction you tried to impose is quite arbitrary.
As to disappearing defenders, they may have simply been banned. This place has become quite similar to UD.
Comment by olegt — June 17, 2010 @ 10:07 am
June 20th, 2010 at 4:19 pm
olegt, if I've not understood your point, please help me understand better.
About viruses, they can get by with no cells of their own only because they depend upon being able to hijack other cells to manipulate them to create more copies of the virus. Thus, they are a parasite, not a self-sufficient organism. That also indicates they depend on cells already existing, and upon the complex multi-molecular machinery of cells already existing.
Consequently, they can shed no light at all on the question of how such multi-molecular machines originated in the first place. That is The Problem that I have been discussing all along — how could this multi-molecular machinery originate in the first place?
I've never denied that there could be change or (non-biological) "evolution" or natural selection operating even at the stage of a hypothetical RNA World. On the contrary, it would be real and would be part of the problem. See my discussion of Dodge #2 in the Handy Reference above.
About Nick, I very much doubt that he has been banned. There has been nothing to indicate that or to give a reason to expect that. Nick is known to come for a while and then go for months at a time.
But I'm glad you are around and engaged. You will notice that I didn't link from Dodge #5 to any of your posts, even those that have similar wording. I didn't because I am hoping you will confirm that you have no intention of begging the question by implying that the advance of science should be equated to vindicating abiogenesis.
Yet you haven't made a clear statement of where you stand in that regard, despite my earlier questions (e.g. here and earlier).
So where do you stand on #5?
Comment by eric not_at_home — June 20, 2010 @ 4:19 pm
June 20th, 2010 at 6:05 pm
You seem to not have addressed the issue we were discussing, namely that Darwinian evolution is not restricted to cellular organisms. A classic example I have provided is the evolution of viruses, which have no cells, yet we apply the principles of Darwinian evolution to them.
Comment by ID guy — June 20, 2010 @ 6:05 pm
June 21st, 2010 at 8:48 pm
p.s. to olegt, I am assuming that in your latest post your only reason for brining up viruses was as support for the reality of selection and change for something other than a cell (though even viruses need to use cells). As I said in my previous post, that much was not being questioned, even at the stage of the RNA World, so it doesn't really affect The Problem at all (cf. Dodge #2).
However, if you were intending to use viruses as some kind of evidence about what would happen in the RNA World, then there is a different problem. Since viruses depend on cells, which depend on the very complex multi-molecular machines whose origin is at issue, to appeal to virus evidence to prop up the viability of the RNA World would be reasoning in an illogical circle. See Dodge #4.
I should thank Nick Matzke for providing not one but two examples related to this dodge — something you once seemed to think no one would ever do and that was merely a straw man.
Comment by eric — June 21, 2010 @ 8:48 pm
June 22nd, 2010 at 2:46 am
eric wrote:
eric,
There is no reason to put scare quotes around the word evolution in the latter context. The same principle (descent with modification) is applied to two different systems (cellular organisms and replicators). The claim is not that the systems behave identically, but rather that the same underlying principle is at work.
Again, the evolution will play out differently in these two contexts. But that does not mean that one needs to invent an entirely new set of ideas. This kind of recycling is regularly done in other fields of science. Energy conservation applies equally well to mechanics, electrodynamics, and elementary particles. The same underlying principle is applied to drastically different systems.
Comment by olegt — June 22, 2010 @ 2:46 am
June 22nd, 2010 at 2:52 am
eric wrote:
Or the reality may be that God created this world five minutes ago and made it look like it's thirteen billion years old. Or it could have been the Invisible Pink Unicorn. Such hypotheses can never be ruled out.
Science has a proven track record of solving problems that looked insurmountable in the past. Does it mean that science will solve every hard problem? No. But I am not saying that. I am objecting to people like you who claim that (*insert your favorite problem*) cannot be solved by science in principle. There is no reason to make that claim.
Comment by olegt — June 22, 2010 @ 2:52 am
June 22nd, 2010 at 8:18 am
I thought it was 4.5x billion years old.
As for an old universe and a young earth, well the designer(s) used relativity.
Except that ain't what we say.
We say materialism cannot solve many issues in principle.
You are conflating materialism with science.
Comment by ID guy — June 22, 2010 @ 8:18 am
June 22nd, 2010 at 8:09 pm
Thanks for responding, but you are not yet answering the question asked.
The question is not whether science will "solve" this question, i.e. advance and come to some resolution about the nature and origin of biological life. The question is whether you are choosing to equate a "solution" with vindication of abiogenesis.
It very much seems that you are trying to equate the "proven track record" of science with the assumption that it will reach the conclusion that life has an undirected origin. This is Dodge #5, which is begging the question — a logical fallacy.
That is unwarranted, since it has never been the case that science always explains everything by undirected law+chance working on matter+energy. Some things (e.g. writing and machinery, the very features we find in cells) are explained by directed causes, not undirected.
I wanted to give you the benefit of the doubt, but you seem unwilling to distance yourself from the logical fallacy of begging the question. Is this what it takes — a logical fallacy — to try to justify the leap of faith in favor of abiogenesis? Science is defined to have an implied promise to side with abiogenesis rather than against it?
Comment by eric — June 22, 2010 @ 8:09 pm
June 22nd, 2010 at 10:49 pm
Multi-molecular Machine Summary So Far — It seems the defenders of abiogenesis have run out of ideas for trying to justify faith in an undirected origin for multi-molecular machines. The responses already made fall into just a few general categories:
A) Show that natural selection is real and that a type of prebiotic "descent with modification" is possible. (True, but nevertheless irrelevant because that is not at issue. What is relevant is that the specific direction of selection in that context is not what they need. The direction is influenced by the inherent limitations of the replication that provides "descent". By its very nature, it cannot replicate multi-molecular structures. Open gondola hot-air balloons can travel, but that doesn't mean we should expect they are suited to take us to the moon.)
B) Pointing to what something else can do (where the "something else" depends on intelligence or else circularly depends on the very multi-molecular machinery whose origin is being discussed).
C) Non-attempts that hide The Problem, e.g. via obfuscation or other rhetorical dodging, such as the logical fallacy of begging the question (cf. recent post and Dodge #5).
The table is still open for New Ideas, but those don't seem to be forthcoming. So far, we don't have any empirical or theoretical basis for a rational conclusion that undirected chemicals in a prebiotic context tend to descend and modify into complex multi-molecular machines. It rests at present on a leap of counter-factual faith despite the available evidence.
Meanwhile, there are other questions concerning abiogenesis that can also be considered. …
Comment by eric — June 22, 2010 @ 10:49 pm
June 23rd, 2010 at 1:33 am
eric,
When has science ever explained anything in terms of "directed" or "undirected" stuff?
I'm aware that, say.. a person with such-and-such metaphysics may assert that phenomena X is ultimately directed or undirected by any mind. I'm aware of secondary arguments, where a given structure (say, the divje babe flute) is argued to have been or not been intentionally created by a human. But I can't think of any *scientific* explanation that rules out, or even considers, direction or guidance in any ultimate sense.
When a scientist drops two items of different weight from the same height, it doesn't seem to me that he's testing idealism, or occasionalism, or Bostrom's simulation theory, or anything else. And when gravity or a fundamental force or whatever sorts of interactions are invoked in a model, I don't see where "…and it takes place with/without any mind's ultimate knowledge or intention or..!" shows up. Not as science.
I get your point, and I'm probably harping on an objection similar to what Daniel Smith (I think) has brought up. But I think you're giving science too much credit. Science doesn't deal in "directed" or "undirected" on the levels you're thinking, it seems to me. Much as many people like to pretend they do. But unfortunately for them, that's philosophy and metaphysics.
Comment by nullasalus — June 23, 2010 @ 1:33 am
June 23rd, 2010 at 2:52 am
eric wrote:
eric,
This is wrong on a very basic level. As nullasalus said, science is not in the business of distinguishing between directed and undirected causes. These are philosophical, not scientific categories. If you wish to discuss philosophy and metaphysics, you'll have to do it with someone else. I am not particularly interested in these discussions.
What scientists working on the problem of life's origin do is orthogonal to this. They posit specific pathways through which life may have arisen and they test their plausibility in conditions that existed on Earth a while ago. Jack Szostak of Harvard and his grad student have written a nice review of the field that a non-specialist can read. You can find it here.
That's how science is done. Scientists do their work not in order to resolve a philosophical question (like the one you are trying to force on me) but in order to gain scientific knowledge. In the process, they make some philosophical questions obsolete. For instance, now that we have a physical theory of electromagnetism, we no longer ponder whether or not lightning is made by a deity. Not that science disproved that, but somehow having a natural understanding of lightning made it less sexy for believers in supernatural (a hat tip to nullasalus).
When (and if) scientists finally figure out how life originated on Earth, your question will become obsolete, too.
Comment by olegt — June 23, 2010 @ 2:52 am
June 23rd, 2010 at 4:22 am
olegt,
I'll have to disagree with you too, olegt. Let's look back at what you've said.
Nonsense. This gets into questions of motivations, into personal understandings of what one's work can or does show, etc. There have been plenty of scientists who did their work to "resolve a philosophical question" or close to it. Hell, you're a physicist, aren't you? Are you really going to say that, for instance… Einstein wasn't motivated in some, maybe much, of his scientific work by a desire to resolve and bolster certain philosophical questions/issues he had?
Science is largely unable to resolve philosophical or metaphysical questions. But scientists are entirely capable of misunderstanding or misrepresenting science in the service of a philosophy, personal belief, or political and social aims.
This is just confused. You yourself said that science didn't disprove who or what "made" lightning (or who or what controls it, for that matter), so the question isn't obsolete. Apparently by obsolete you only mean "less sexy", but in that case "science" has nothing to do with it. That has more to do with culture and subjectivity.
What's more, science doesn't simply plod on, where there's a static number of questions X constantly being transferred to "answered question" pile Y. New questions get opened up. Quantum physics upended ideas about the "material" so thoroughly that even self-styled physicalists are now spooked enough about committing to too certain a view of matter that full-blown panpsychism is now considered a "physical" (even monist!) theory. Advances in computer science opened up another design route, to the point where we have guys like Nick Bostrom suggesting that it's possible we live in a simulated universe, and guys like John Gribbin suggesting we live in a designed of a different type.
But that opens up even more problems: Gribbin and Bostrom both consider themselves to be naturalists, and their theories to be naturalistic. And they can easily do that for one reason: "Natural" and "Supernatural" are poorly defined terms that are mostly used for effect, not to enlighten. You know, to make things more or less sexy.
Well, even the lightning question wasn't made "obsolete". Just "less sexy". That must be what you mean here too.
But even there, who's to say science will make the question "less sexy" to one group or another – especially intelligent design proponents? Hell, I'm sure plenty of ID proponents would argue that science has made the origin of life (and numerous other scientific inquiries) *more* sexy to them by uncovering minimal thresholds for cell operations, the number of imagined coincidences that have to be in place for abiogenesis to get off the ground, the success of intelligent agents in implementing these coincidences in the lab, etc. Why this assumption that whatever science will uncover will ultimately go a certain route, or have a certain effect? Again, if one would have said that years before the OoL was studied in greater detail, they'd have been dead wrong.
Science can't resolve the ID question, just as it can't resolve most other metaphysical questions. It can't even, on its own, make certain views or positions "less sexy" – that's a function of spin, philosophizing, and cultural forces. And it hasn't shown what "unguided processes" or "guided processes" can do, because science* is incapable of determining what is or isn't guided anyway.
(* Unless personal philosophizing or importing of metaphysics is considered 'determining'. In which case, hey.. open season for all sides I suppose.)
Comment by nullasalus — June 23, 2010 @ 4:22 am
June 23rd, 2010 at 4:53 am
nullasalus,
The word obsolete was meant in its usual sense, no longer in use or no longer useful. The question of whether or no lightning is directed by someone is not frequently discussed as far as I can tell. Obsolete it is.
I don't particularly care what philosophers think about quantum mechanics. By and large, they don't understand. Bostrom's simulation hypothesis is another tempest in a philosophical teapot. I haven't heard of Gribbin's suggestions, so I won't even comment on that.
As to what makes a topic sexy to
cdesign proponentsists, a known aphrodisiac is the lack of a well-established scientific theory. Physics of the sun used to be sexy. Now that the puzzle of solar neutrinos has been resolved, the bloom is off the rose (see Arguments we think creationists should NOT use ).So it is with other topics. Creationists have largely abandoned the issue of whether or not evolution occurs (even YECs). Fewer and fewer voices dispute common descent of humans and apes. Creationism marches forward, wherever science's leading edge takes it.
Comment by olegt — June 23, 2010 @ 4:53 am
June 23rd, 2010 at 5:34 am
olegt,
That's even worse for you, Olegt. You yourself said that science has not (and you implied, reasonably, that science could not) settled the issue. If your standard of obsolete depends on whether or not anyone thinks that lightning or other phenomena is ultimately guided, you were flat out wrong to call it obsolete – there's a hell of a lot of people who believe in an omniscient and omnipotent being, and a surprising number who are open to the existence of designers who would be called gods in any other age.
Now, maybe you'll say "Well, it's not discussed by scientists!" But since science has zero to say there anyway, and it's never been offered up as a "scientific" theory…
Who said philosophers were the only ones talking? The physicists alone talking about the philosophical aspects makes a considerable list. Richard Conn Henry. Henry Stapp. Roger Penrose. Bohm. Etc, etc. I know you yourself say you have no interest in philosophy – but plenty of physicists, frankly, will not shut up about such things.
Let me guess: More tempests in teapots? We're going to need to build more shelves to store all those damn things on at this rate.
Or the development of scientific theories which comport well with their ideas (See: The discovery of the genetic code, the big bang theory, fine-tuning arguments, etc, etc.) This question goes far beyond YECs, or really, even beyond the traditionally religious. ID in particular has made it so the question is no longer "Did a designer do it or did evolution do it?" – evolution is just one more tool for a designer. Hell, it's a tool we use ourselves.
But that's neither here nor there. Science runs both ways on this topic, and the assumption that scientific discoveries can only be used to encourage one side in this dispute is false on its face. Plenty of ID proponents out and out love what they've been seeing out of the sciences for the past few decades on topics ranging from cosmology to biology to computer science to information theory to otherwise. We're going to need more teapots for these tempests.
Comment by nullasalus — June 23, 2010 @ 5:34 am
June 23rd, 2010 at 7:20 am
you've got to get out more
check this out
peace
Comment by fifth monarchy man — June 23, 2010 @ 7:20 am
June 23rd, 2010 at 7:41 am
No, fifth monarchy man, I am afraid that debates about whether lightning is the wrath of God ended in the late 18th century.
Following Ben Franklin's discovery of lightning's physical nature and his invention of the lightning rod, Christians at first resisted the installation of this simple device for theological reasons. By installing a lightning rod one sins against Him by resisting divine punishment. Ironically, it was churches that suffered most from lightning strikes because they would often be the tallest structures in town. So after a few decades of resistance, lightning rods were installed in churches and lightning-induced fires stopped.
Of course it made no sense to treat lightning as God's wrath any longer. If a fallible human can effectively deflect divine punishment then God is not omnipotent. So it made no sense to regard lightning as the wrath of God. The link you provide only makes a jocular reference to that interpretation. The church has decided to rebuild the statue anyway, so it either did not get His message or did not think it was from Him.
Comment by olegt — June 23, 2010 @ 7:41 am
June 23rd, 2010 at 8:22 am
Two assumptions being that prior conditions were sufficient to generate causal outcomes and that there is no possibility of refuting that prior assumption with physical evidence drawn from nature itself. That's why there cannot be a minimal genome concept when minimal refers to more than gene number. Minimal cannot challenge the sufficiency assumption. There can be no possible physical evidence for minimal where sufficiency is concerned under the rules of engagement. Minimal would have to be presumed as attributable to a lack of knowledge rather than based the nature of physical conditions. Just so we recognize what is going on.
Science analyzes how a watch functions. It does so in fine detail and incorporates energy and matter concepts within the mechanical explanations. What science cannot do is explain the existence of the watch within anything other than a sufficiency of prior conditions concept. Therefore the intelligence and consciousness of the watch's creator must always be linked to a mindless physical origin. It's the rules of the game or the philosophical context if you will. Lightening was akin to a spring in the watch. Analyze and explain. The capacity for abstract intelligence. Analyze and explain within a sufficiency presumption. Go ahead. Give it your best shot. It's all found in mindless chemicals. No philosophy right? Pay no attention to the man behind the curtain.
Comment by Bradford — June 23, 2010 @ 8:22 am
June 23rd, 2010 at 9:36 am
Of course it is.
One of the main questions that science asks is how did it come to be this way?
They do their work in order to understand reality.
They have accepted evolution occurs for at least two hundred years.
That is nothing but a bald assertion.
And there still isn't any scientific data to support the claim of common ancestry between chimps and humans.
It isn't taking to towards universal common descent.
Comment by ID guy — June 23, 2010 @ 9:36 am
June 23rd, 2010 at 8:03 pm
While olegt claims to not be interested in philosophy, we can all tell what his philosophy is by his interpretation of empirical facts.
Funny how that works.
Comment by Daniel Smith — June 23, 2010 @ 8:03 pm
June 23rd, 2010 at 9:45 pm
My apologies. I don't think you did get my point, probably because I was not being clear. I wasn't referring to any esoteric metaphysical point. It is something much more mundane and routine to the ordinary practice of science.
When a scientist discovers an arrowhead, it would be absurd to think it a "failure" of science if he cannot explain the arrowhead as the result of erosion and other undirected processes of nature. Rather, the science recognizes that it is an artifact and treats it as such.
Likewise, if a scientist finds ancient writing, even if there is no translation and the author is unknown, there is no implied obligation that the only "scientific" posture is one that explains the writing as the result of a natural undirected chemical process of ink. Similarly, it is not a "failure" of science to recognize a mechanism dredged from the sea floor as an artifact, or to treat ancient tools as artifacts, even if we do not understand their intended functions.
The logical error of begging the question takes place when it is assumed that "scientists finally figure out how life originated on Earth" can be treated as a synonym for "scientists conclude that life arose on Earth from an undirected process of nature".
You see, such a view assumes that the only correct scientific conclusion must be that abiogenesis is the explanation for the biology we see. It assumes that either science will figure out how abiogenesis works, or else perhaps that science will just be stumped.
The history of progress in science is then invoked to give supposed encouragement that science will not be stumped and (therefore) will find out how abiogenesis did it (which again begs the question by assuming that abiogenesis did it).
This completely ignores the fact that science has never been obligated to explain everything by law+chance apart from intelligence. When appropriate, science has routinely succeeded and progressed by recognizing artifacts of intelligence for what they are.
Of particular importance, unlike anything else in nature that we have explained using law+chance, cells contain both symbolic information and complex machinery — two categories of effects that science has always previously explained as the result of intelligence, never as the result of blind law+chance.
So the idea that the "track record" of science is on the side of abiogenesis is simply false.
Comment by eric — June 23, 2010 @ 9:45 pm
June 23rd, 2010 at 11:03 pm
eric,
No, you're plenty clear. And I agree with your point: Yes, the measure of "successful" science isn't from finding an explanation that makes no reference to intelligent agents. To attribute to operations of nature what an individual was in fact responsible for wouldn't be an advance of knowledge.
My comments were directed at wording like this…
I'm saying that no scientist has ever identified any "undirected processes of nature", period, as a scientist. Certainly not undirected in the sense you must be speaking of (by a designer(s), or The Designer, so to speak). Scientists can identify processes in the abstract. It can investigate whether such processes may or may not have taken place, or what said processes could accomplish in the normal course of events, etc. But whether those processes are directed? Undirected? That's philosophy and metaphysics. Stuff scientists as scientists steer clear of, as much as possible.
And to be clear: I know your past response has been that (and I think this is Dembski's line), yes – in principle, everything may ultimately be designed and guided, no matter how normal or commonplace. ID focuses on particular cases, (paraphrasing here) things we know intelligent agents are capable of, but what we've never seen happen in the normal course of nature. Hopefully my understanding of that much is accurate.
I'm saying that adding "undirected" in front of "processes" adds nothing to the description – it's gratuitous and assumed, not demonstrated, and probably is undemonstrable within science besides. And I know you're not trying to advance one metaphysical view or another when you say that, certainly not naturalism. I just see it as a mistake to think and speak in those terms, even if it's done so commonly. It helps add to the misconceptions people have about science, what science has or even could demonstrate, etc.
But again, I really do get and otherwise agree with your point about artifacts versus "nature".
Comment by nullasalus — June 23, 2010 @ 11:03 pm
June 23rd, 2010 at 11:05 pm
p.s. to all — see also Dodge #5 regarding how the logical fallacy of question begging is applied to the origin of multi-molecular machines.
Even those who suppose naturalism is true don't have a logical leg to stand on to justify begging the question.
1. Even if it is supposed that there exists an undiscovered natural process capable of leading all the way to intelligent agents such as ourselves, we have no basis for claiming this undefined, undiscovered natural process would only exist on Earth or that we are the first intelligent beings in the universe.
2. If our biology is nothing more than the result of such a process, we have no logical basis for supposing it impossible for us or any other sufficiently advanced intelligence to engineer living organisms (and we seem well on our way to attempting to do exactly that).
3. In light of points #1 and #2, even supposing naturalism were true, it would still be the case that our own type of biology could very well be the result of an earlier designing intelligence. It may be that the biology we see can only occur as a result of intentional direction.
Thus, even supposing naturalism, the idea that our biology requires intelligent design cannot be excluded. And if that were indeed the reality regarding the origin of life of Earth, that would not mean that science must "fail" because all abiogenesis explanations were wrong. Rather, the success of science would simply mean recognizing the fact that our biology requires design.
This exposes the question begging logical fallacy of assuming that scientific success can be equated with finding out how abiogenesis made life on Earth — even if one supposed naturalism is true.
True science is never an obligation to deny reality. Legitimate science is never slavery to assuming someone's favored story.
Comment by eric — June 23, 2010 @ 11:05 pm
June 23rd, 2010 at 11:19 pm
nullasalus, just saw your latest post after posting my last one.
Yes, the question you are raising is indeed much like the one Daniel Smith has raised and that is indeed a metaphysical / philosophical question that science does not appear to be in any position to answer. So I think we are all agreed about that.
By "undirected" I don't imply any particular answer to the question you raise. In this context, "undirected" is understood to mean "operating according to the built-in, innate regularities of matter and energy apart from any detectable intervention of an intelligent agent to direct the effects otherwise".
Now, I do recognize that the wording "undirected" is considered by some to convey or imply something about those larger metaphysical questions that are beyond the reach and sight of science, and so that wording is also considered to be unhelpful and preferably avoided.
So here is the problem. What wording would you suggest that is equally concise and at least as clear at specifying the absence of intervening intelligent direction beyond the normal innate regularities of matter and energy?
For example, Dembski sometimes uses "natural process" to convey this idea, but that lands into the problem that some assume the complementary category always implies something supernatural, which is incorrect. So that seems even worse.
Comment by eric — June 23, 2010 @ 11:19 pm
June 23rd, 2010 at 11:32 pm
I seems my wording may have misled you with regard to my point, since I was not addressing esoteric philosophical issues outside of science (as you seem to have thought).
If science could not distinguish between the categories that I am talking about, then scientists would be obligated to explain Stonehenge as the result of geological processes of nature, rather than recognize that it is the work of intelligent agents. This would be absurd.
For science to function in a reasonable manner, the distinction I am talking about is a necessary one to ordinary scientific operation. It would be dysfunctional nonsense if scientists could not distinguish between the categories of what is and what is not an artifact of intelligent agency.
The point this leads to is that there is no legitimate justification for begging the question by assuming scientific progress is equivalent to vindicating abiogenesis. The actual "track record" of science is to infer intelligent agency for symbolic information and for complex machinery.
Comment by eric — June 23, 2010 @ 11:32 pm
June 24th, 2010 at 4:31 pm
eric,
Actually, upon reflection, I think I'll avoid getting to deeply into that for now. I have ideas and suggestions, but I don't want to pry this discussion off in too different a direction just because of my particular criticism/hobby-horse of modern ID / "nature" / etc debates. That's a subject for a whole different thread.
I'll just say that I think one of the biggest problems in these discussions is that science doesn't/hasn't/damn-well-possibly-couldn't show what many people think it did/has/can. I don't need to lecture you of all people on the importance of knowing where philosophy ends or science begins. You know, you focus on important presumptions and misconceptions rather handily, etc. I'm just a stickler for language, because I think that helps cause a lot of these problems to begin with.
Comment by nullasalus — June 24, 2010 @ 4:31 pm
June 27th, 2010 at 12:05 am
I meant to point out earlier that there is a very good reason for doing whatever is necessary to more clearly distinguish between the two cases of biological evolution and abiogenesis. Nick Matzke showed why.
1. While it might be clear to you that there could be a significant difference between the two contexts, Nick repeatedly reasoned as though evidence from one told us what the other was capable of (cf Dodge #4). Whether intentional or not, the equivocation pivoting on words such as selection or evolution played an important role.
2. Nick even went so far as to imply that this problem has already been dealt with — a "million" times — while in fact confusing biological evolution with the distinct context of abiogenesis (cf. Dodge #6).
3. These two distinct contexts appear to be so completely confused, muddled and mixed together in Nick's thinking that it also appears that he has never before understood, let alone seriously considered, this serious issue for abiogenesis. He shows no awareness that the distinct context of abiogenesis might have insurmountable difficulty where biological evolution might not. In Dodge #1, notice how for him this issue is new and unfamiliar. He says, "… now there is this bizarre argument …" — and even then cannot manage to describe the issue correctly. Either this is willful obfuscation, or else he had not yet comprehended the distinct problem of this distinct context.
As long as matters are as muddled as this, there are very good reasons to make every effort to illuminate the distinction in these very different contexts.
Comment by eric — June 27, 2010 @ 12:05 am
June 27th, 2010 at 3:28 am
What's next, eric? Different number systems for counting apples and oranges?
Comment by olegt — June 27, 2010 @ 3:28 am
June 27th, 2010 at 9:01 am
I take oleg has different number systems for counting his fingersa dn toes…
Comment by ID guy — June 27, 2010 @ 9:01 am
June 27th, 2010 at 10:02 am
What's next is seeking a clear statement from you on whether you see anything wrong with Nick implying that the behaviors of the two distinct contexts are essentially interchangeable and undistinguished. You wrote:
Yet Nick reasons as if they are one and the same. Take away the equivocation and his argument falls apart, since it did nothing at all to show that the way "the evolution will play out" for the RNA World would lead toward (rather than away from) complex multi-molecular machines.
When I earlier pointed out what he was doing, I asked you:
Amazingly, your reply then was this:
So which is it? If someone tries to treat the "two different systems" as though the behaviors and capabilities are interchangeable and evidence of what happens in one is sufficient to show what the other would do, do you still find nothing objectionable in that? Nothing at all?
Comment by eric — June 27, 2010 @ 10:02 am
June 27th, 2010 at 2:08 pm
eric, you are recycling your old complaints. They were addressed by Nick here. I commented on that here. I have nothing to add beyond that. Cheers.
Comment by olegt — June 27, 2010 @ 2:08 pm
June 27th, 2010 at 8:15 pm
The problem with what Nick said is that in order for RNA to do anything there must be two strands- one to act as the template and one to act as the catalyst.
It is not self-replication.
And there isn't any evidence that either can arise via blind, undirected chemical processes.
Also oddly enough the RNAs that were synthesized to bring about this replication system did show signs of change in sequence but not a change in function.
IOW replication and variation didn't accomplish anything.
At least Darwinian evolution can break things…
Comment by ID guy — June 27, 2010 @ 8:15 pm
June 29th, 2010 at 10:23 pm
No. Rather, I've asked you to take a clear stand on whether you find truly nothing objectionable about Nick's pointing to biological evolution with the implication that it shows what would happen in the distinct context of RNA World replication.
It is revealing that you seem either unable or unwilling to do so, and prefer to excuse yourself from what should be an easy question.
Everything Nick said there was refuted and exposed as dodging the actual problem here.
1. He defends the influence of natural selection, which is irrelevant because it's influence was never denied. In fact, it is part of the problem. See Dodge #2.
2. He equivocates on the meaning of "machinery" thereby redirecting attention elsewhere while entirely failing to address the actual problem of multi-molecular machinery. See Dodge #1.
3. He tries to support his position by linking to irrelevant evidence from biological evolution. See Dodge #4.
4. He closes with another attempt to redirect attention elsewhere by making reference to "complexity" — again without even touching on the actual issue of multi-molecular machinery. See Dodge #1.
Did Nick anywhere in this thread ever give any explanation of actually how the RNA World would go about promoting multi-molecular machines? No, none at all. After subtracting all dodges, we are left with Nothing. Zero.
In fact, he never even once correctly described or accurately acknowledged the actual problem being posed. Not once that I can find. Every description from Nick misrepresented the issue. It even seems as though he has never considered the problem (it is a "bizarre" new argument to his mind), and even then apparently does not comprehend the nature of the issue. He persists in thinking it is something else.
That is where you said:
Yet, if we take your point seriously, this undercuts the defense offered by Nick. Your two positions are contradicting each other. All his appeals to the outcomes for biological evolution depend on supposing evolution would play out similarly for RNA World replication, not "differently" as you stated. Yet you apparently wish to persist in finding "nothing objectionable in it."
It seems you are either unable to recognize that Nick is violating the standard you professed, or else perhaps unwilling to clearly acknowledge that he did so or that this destroys the relevance of citing the outcomes for biological evolution.
It would be a very simple matter to acknowledge Nick's failure. It is not as though you said all that he said. Yet you cannot bring yourself to do so. Amazing.
Are arguments evaluated only according to the conclusions they reach?
Comment by eric — June 29, 2010 @ 10:23 pm
July 2nd, 2010 at 11:21 pm
No, I don't agree. There are multiple severe issues.
[Sorry I didn't answer before that thread closed. I hope you find this answer. This thread seems more fitting in any case.]
1) First, attaching amino acids to RNA triplets does not speed replication. On the contrary, it would inhibit replication. This fact is evident from the inherent nature of how RNA replication works. It isn't something we just don't know about or can work out later.
The first step is to bind the bases of the RNA strand to complementary nucleotides, forming an "opposite" strand (i.e. the reverse complement of the original). This cannot happen so long as those bases are bound to anything else. They must be free to bind with their individual complements. (Then, if the same process happens to the reverse complement, you then get back to a duplicate of the original. Here again, the bases must be free to bind with the complementary nucleotides, or the opposite strand cannot be constructed.)
This is why natural selection in the RNA World is the enemy of complex multi-molecular structures. It will preferentially favor the multiplication and increased frequency of those strand sequences that best avoid becoming unavailable for replication due to competing attachments.
2) Increasing speed does not automatically mean move faster toward those things that cells need. As in the previous point, it can also mean moving away from such structures. Without scrutinizing actual direction, speed is an insufficient consideration.
3) The presence of amino acids in an uncontrolled environment, i.e. one were neither cells not scientists are directing events according to a preexisting plan, cannot be assumed to automatically be beneficial — even though cells obviously need amino acids. That is why investigators interfere and create artificial conditions that are not realistic. Here is an example of Interference Strategy #1: Eliminate the Undesirable Chemicals:
(For more on this and other methods of interference that are employed to avoid unfavorable chemical consequences, see the summary list here.)
4) Even if we suppose in sheer faith, completely without skepticism or scrutiny of any kind, an RNA World that finds some unspecified favorable utility in having various amino acids bind directly with certain RNA base triplets, the idea that any such system (using the term very loosely) could be slowly and gradually migrated to employing suitable tRNA molecules appears to be utterly unworkable.
Anyone who has tried to convert any system to operate according to a new convention should be able to see the issue plainly. How does mystery function X still function while you have incompatible and inconsistent intermediate states? And once you have intervening nucleotides of RNA (so the direct binding is lost — in tRNA the codon + anticodon pairing is entirely independent from the other end of the tRNA where the amino acid binds), how is this accidental association preserved while the set of tRNA are supposedly being "developed"? The problems compound when one notes that the bodies of tRNA are not arbitrary. In a ribosome, they are specialized and distinct to satisfy kinetic considerations and for the translation to work.
I think it would be easier and more plausible to believe in unicorns or that pigs can fly than to suppose that such a system of conventions would develop and proceed to the final state without intervention that is pursuing a goal.
Keep in mind that chemicals as chemicals can be quite content at stopping with chemicals binding to other chemicals — even if it leads only to lifeless tar and gunk, or "very long chain polymers" that would exclude life. Chemicals don't need to make a cell, and there is no evidence that they try to do so.
Comment by eric — July 2, 2010 @ 11:21 pm