Fossil and Evolution

[articulett]

That's not what a real DNA molecule looks like just so you know. It's what the diagram looks like which we depict the double helix as. Normally the DNA is totally twisted up and folded.

The bacteria in this case is interesting. Spirochetes themselves are a common bacteria.

Yeah, I know...but the structure is interesting--with the second strand...and yes, I know what DNA looks like and how it winds and unwinds and condensces and becomes spaghetti like...I'm just curious about some of the forms that seem to repeat in life...like left handed chirality...diatomes have some really interesting shapes too--I posted it with the hope that maybe someone here might have seen something similar because the guy who found it is looking for any information out there. I really like that web site--some great photos!

 

[articulett]

This is a great video from Nova Science Now regarding life from non-life

http://www.pbs.org/wgbh/nova/transcripts/3214_sciencen.html#h01

It includes a transcript including an interview with Francis Collins.

And here is some recent news on chimeras. Chimeric twins were born from a single ovum that was fertilized with 2 spermatazoa. http://web.mac.com/aranyak/iWeb/Aranyak/evolution/E725FC9A-B498-470E-9BB3-0967A589A0E7.html

http://www.springerlink.com/content/m5q6420770g60643/

(this is another way that genomes can be altered...I include it because I had mentioned it earlier...)

I think that will show you why this recent experiment is so exciting...

So will this: http://space.newscientist.com/channel/astronomy/astrobiology/dn2100

It means that the building blocks for life are robust--and may be prevalent in our universe-- Nucleic acids can and do form on their own--so do "containers"--cell walls (see video)--

those with a vested interest in proving evolution wrong or murky or in need of an intelligent designer will not be eager to see or learn of these discoveries--so it's hard to share the significance with such people. It's like Behe with irreducible complexity--nothing is never ever enough--creationists never cede. And it gets maddening. They keep pointing to flaws and asking questions and refusing to "compute" the answers, but don't offer clarification or better explanations or anything.

How can it be a dialogue of discovery if one person has an unadmitted emotional investment in thinking that evolution must be flawed? The creationists naysay and ask for proof and then declare that absolutely no one answered their question--no matter what effort people have gone through. I just don't think it's honest. Nor is it honest to call Evolution a dogma. Is the atomic chart dogma? Evolution is more supported than the atomic chart. Creationist have a strong belief that scientists are all biases and looking through the dogma of Darwinism--but they never ask themselves if maybe, just maybe, their "intelligent designer" is an illusion--and an illusion keeping them from understanding and celebrating human discovery.

I'm not jumping through any more hoops for creationists. And I don't care if you deny the label--or dodge the wording...we CAN tell--because ABSOLUTELY NO ONE can answer your question. And that is because you need that question to remain unanswered.

Check out a link and ask a real question with a hint as to what sort of answer you are hoping to find if you want a real discussion. Deceptive questions are just a crappy way to waste peoples' time. And it's worse when you insult them for their efforts at careful and detailed explanations and links you never visit. Respond to what people say, if you want a true dialog. And don't ask questions if you have no real curiosity in having that question answered...and quit calling evolution "dogma"--it's only "dogma" to creationists. In science, it's a fact.

 

[Ichneumonwasp]

Why do you think that a templateless replicase producing oligonucleotides is an example of abiogenesis or at least how abiogenesis occurred in the primordium?

It is seems that you are overinterpreting the results of the paper. The investigators took a preexisting molecule of one type (in this case a protein) and had it produce a molecule of a different type (in this case an oligonucleotide). There was no self-replication, which at least form how I understand life, is an important, and maybe the defining, aspect of life, along with self-organization. To be fair, it was interesting that the different conditions produced oligonucleotides with different properties, which implies some sort of "adaptation", but there was also no mention of them being self-replicating.

I think that the discussion would be much more productive if we came up with a working definition of "life" so that we could then in turn define "abiogenesis". Right now, I feels like we're talking circles around one another because we don't have a common ground from which to start. This allows us to deny one another's definitions and cry "creationist" instead of learning from one another.

Dr A's response was a bit tongue in cheek, but the importance rests in overcoming a conceptual hurdle. Neither I nor anyone else said that the paper showed self replication, but the conceptual problem frequently trotted out by the "you can't get there from here" crowd is that self assembling nucleotides just are not possible. But, if life started with peptides that could serve as templates for nucleotides to assemble in small chains, those nucleotide chains could serve as templates for self-replicating entities.

No one says this is how life began. But it certainly demolishes one of those "there is just no way that life could arise from non-life" probabilistic "calculations" that many IDers love to produce.

To recap......instead of "all you've got it a bunch of amino acids in a beaker -- that isn't life", what the picture with only a little investigation shows now is:

1. Creation of amino acids through natural means.
2. A peptide that can serve as the template for nucleotide chains
3. Nucleotide chains can serve as templates for the formation of new nucleotide chains
4. Self-replicating entities are theoretically possible

So, again, no, no overinterpretation. No one is saying that all the gaps in abiogenesis have been colored in, but that one of the biggest problem is dealt with -- how to organize chains of nucleotides (and potentially why we have the close association of RNA and proteins). We already know that RNA chains can serve as enzymes. And the move to enclosure in lipid membranes is very easy since liposomes form on certain types of clay. The jump to membrane enclosed collections of proteins and self-replicating nucleotide chains is small compared to some of the other developments -- like the formation of nucleotide chains and their close association with protein.

We're talking about a billion years here. A billion years to move from amino acids to the first cells or protocells. The process is looking easier and easier with each step in knowledge.

ETA

Oh, sorry, Articulett beat me to it.

ETAETA

I think that the discussion would be much more productive if we came up with a working definition of "life" so that we could then in turn define "abiogenesis".

Good luck. What you will find is, like all "boundaries" in nature, any definition will be necessarily arbitrary and unsatisfying. It might make more sense for us to relinquish the idea of "life" being special. We create these arbitrary boundaries with language and treat them as inviolable. Our language creates philosophical "problems" (see the Mind-body problem for the most obvious "intractable" example) that we treat as "sacred". Pity that we can not all be new Einsteins and see problems through to their logical conclusion. We give up too easily because we don't like the answers even though the answers when the problem is carried to its conclusion are much more interesting, I think, than any of the lies we like to tell ourselves.

ETAETAETA

And a little searching reveals work on the formation of peptides without the aid of enzyme systems, interestingly enough, not in earth based systems: peptide formation

And this

So, really, we have amino acids that can form naturally. We have peptides that can form naturally. We have certain proteins that can catalyze the formation of nucleotide strands. Nucleotide strands can catazlye the formation of new nucleotide strands. What is missing?

 

[VonNeumann]

Since how abiogenesis occurs isn't known, how can this conclusion be known?

We have the theory of evolution. And there are a number of hypotheses regarding abiogenesis.

Reminds me of when I ponder the Universe. Trouble is I ponder it with little expertise in cosmology or physics. My expertise is in microorganisms that cause disease. Because that involves a heavy dose of genetic science I can say with confidence, your pondering shows little expertise on how the mechanisms of evolution work.

You claim the RNA hypothesis has been discarded. My understanding is all that has been questioned is how did you get to the RNA? In other words it didn't go back far enough. But Joyce demonstrated you can go from free RNA molecules to something resembling the material one considers living. And we have a great number of RNA based viruses.

The smallest genome listed on this site contains 10 genes and 5,386 base pairs. For a bacterium this Live Science article cites the "Carsonella's genome codes for 182 proteins." But you also have some unknown steps those protolife forms could have gone through that we just have not yet discovered.So you just can't go off making claims the probability is improbable. You don't know what processes occurred that could have acted as catalysts or how symbiotic chemical reactions played a part.

If Mike is accused of murder and the detective says he is guilty, the detective will have to show how Mike might have gotten to the crime scene. But Mike's lawyer says Mike was a thousand miles away an hour before the crime but has no alibi for the crime itself. The detective says "we don't know what processes occured that could have acted as [means for Mike to have gotten to the crime scene and back to where he was in a short period of time.]" (note the quote is partially from what you said about abiogenesis).

I'm acting as Mike's lawyer, showing that, with the gap of evidence that shows how Mike could have gotten to the crime scene, he would have had to travel faster than the speed of sound. The detective says "it is possible to travel faster than the speed of sound". The detective is on better ground showing Mike is guilty than we are in showing that abiogenesis could have happened by chance aided by some autocatalytic mechanism that springs also from chance.

When it comes to abiogenesis, we only have hypotheses like autocatalytic sets. No one knows how simple or complex the minimum autocatalytic system needs to be.

You agree we haven't enough theory on this and I agree. So I calculate the probability to jump a gap much much smaller than from amino acids to DNA (or RNA of equal size or protein of equal size). A sequence of 400 symbols, 4 in a set, is a huge leap. Everyone should do some calculations like this to put this in perspective for themselves. What they conclude from it is up to them.

 

[VonNeumann]

You could take the link I provided above or delphi's link and they'll both lead you to the Hox essay on pandasthumb. Here's a direct link to the Icons of Obfuscation response on Miller-Urey.



You completely misunderstood what I meant. "Well's work is so shoddy, it shouldn't warrent mention on forums like JREF (meaning people posting here should know better than to cite it as authoritive), except to note how shoddy it is (i.e. to point out the flaws and errors)"

That's fine with me, but something that you might have said would be a very specific example of what you think this guy did that was "so shoddy."

 

[VonNeumann]

No it wasn't Crick. It's some guy the IDers and Creationists always cite as having done the math. I'll have to find it. It isn't like it was a memorable discovery.

You guys!

No... it WAS Crick.

Crick wrote a book in the early 90's. What was it... "Life Itself" ? I'm not going to look it up right now.

Crick came to doubt evolution could have happened on earth without being previously developed somewhere else. Then he posits that life was directed here, like with spores via interstellar travel of some kind. Kind of like Hoyle and others have mused.

So... YES: Crick!

 

[VonNeumann]

No, you don't understand.

You continue to adopt the "design mindset." Consequently, your analogy above is false, because you presume, a priori, that there is a subset of some total possibilities from which an organism will eventually arise to finally discuss the issue in this forum.

The above premise is simply false. We cannot work backward from our present state and estimate the odds of our being here, any more than we can estimate the odds of a ball falling into the slot of a roulette wheel containing no slots.

Prior to the universe existing, the odds of any particular future event occurring are equal, because given a set of limitless possibilities, all outcomes are equally likely.

To correct your analogy, you would have to take an infinite set of possible letters of infinite combination and then estimate the odds of an infinite number of possible stories of infinite length written in an infinite number of possible languages.

What are the odds of everything happening by chance, when selected from a set containing all possibilities?

Unity.

We are here, because it is inevitable, and it is not philosophy to say so. What IS philosophy is to say that "we" must be of some particular composition/nature, because we could have been anything, in any shape, size or composition.

If we had appeared in some other universe, made of gold instead of carbon, and the entire universe was constituted in a manner which permitted this, then that's what we would be.

Design is only meaningful in view of actual knowledge of the designer -- otherwise, given that infinite set of possibilities, even the designer's proverbial Boeing 747 could have occurred by pure accident in a universe which looked exactly like a junkyard.

Such a thought is only absurd, because we are here thinking such a thing from our perspective, But, in the universe where the 747 sits alone in the blackness of space, it's completely rational -- and in fact, it's the only possible outcome.

You have limited yourself to a mindset which prevents you from accepting that random chance can explain everything. Everything, that is, except for God, because God is the literal antithesis of randomness. If God exists, then randomness cannot, because God must know all in order to be God -- and randomness eschews all possible advance knowledge.

To bring this back to your English story analogy, could one million monkeys with typewriters bang out the complete works of Shakespeare, given sufficient time?

The answer is unequivocally, Yes. In our universe, this incredible accident actually occurred -- accomplished not by one million monkeys, but by only ONE!

His name, of course, was William Shakespeare.

N.B. And, he did it with a quill pen!

I'm sorry but... We use statistics to calculate likelihoods all the time, on events that have already occured. Sure it is P=1.0 after the fact, but at some time in the past it was not.

It's funny you say "The answer is unequivocally, Yes. In our universe, this incredible accident actually occurred -- accomplished not by one million monkeys, but by only ONE! His name, of course, was William Shakespeare."

In a debate on "design", perhaps you'd be dismissed for having uttered a blunder of the first kind. Shakespeare is an intelligent designer.

 

[delphi_ote]

We'll have to agree to disagree. Because I think it was helpful to call you out on this.

I know you like to imagine you're scoring rhetorical jabs with your subtle wit over there, but your complete incoherence makes whatever point you're trying to make impotent.

Here in reality, I'm afraid we'll have to agree that you're wrong. We're in a thread right now talking about creationists and with creationists. Do you have a problem with my pointing out a flaw in their approach?

 

[delphi_ote]

If Mike is accused of murder...

What's the deal with people who believe wierd things using analogies in debates? Why can't they just discuss the topic? Anyone else notice this trend?

 

[Ichneumonwasp]

If Mike is accused of murder and the detective says he is guilty, the detective will have to show how Mike might have gotten to the crime scene. But Mike's lawyer says Mike was a thousand miles away an hour before the crime but has no alibi for the crime itself. The detective says "we don't know what processes occured that could have acted as [means for Mike to have gotten to the crime scene and back to where he was in a short period of time.]" (note the quote is partially from what you said about abiogenesis).

I'm acting as Mike's lawyer, showing that, with the gap of evidence that shows how Mike could have gotten to the crime scene, he would have had to travel faster than the speed of sound. The detective says "it is possible to travel faster than the speed of sound". The detective is on better ground showing Mike is guilty than we are in showing that abiogenesis could have happened by chance aided by some autocatalytic mechanism that springs also from chance.

When it comes to abiogenesis, we only have hypotheses like autocatalytic sets. No one knows how simple or complex the minimum autocatalytic system needs to be.

You agree we haven't enough theory on this and I agree. So I calculate the probability to jump a gap much much smaller than from amino acids to DNA (or RNA of equal size or protein of equal size). A sequence of 400 symbols, 4 in a set, is a huge leap. Everyone should do some calculations like this to put this in perspective for themselves. What they conclude from it is up to them.

I'm afraid that I don't see how this analogy is in any way applicable. You are taking a situation in which you know the probabilities (essentially 0%) and using it as an analogy with a situation in which you know none of the probabilities (at least not in any substantive sense).

The number of symbols in a particular sequence is meaningful only (and I mean only) if the end target --those exact symbols -- is what one is after. With biogenesis there is no direct target. There is no known quantity that makes life possible. We don't know how many peptide chains could serve as templates for RNA assembly (we know at this point that one definitely can). We don't even know if this is how things occurred, only that it is a possibility. Since we know that amino acids can form from natural substances (100%) and that peptide chains can form from natural processes (and that it is the initial peptide linkage that is critical) (100%), and that with some peptide chains RNA assembly is possible (100%) where is the problem? With one billion years to work out combinations that lead to increasingly complex combinations -- with the winners surviving? Chance is correct in the first instance -- the first peptides to form, but complexity and selection follow ever afterwards. How do you model that in your probabilistic scenario?

ETA

Actually, let me rephrases the above. You have used an analogy in which we have no known possible mechanism for someone to have performed some action and employed it in a situation in which we have already provided potential mechanisms. We have provided the mechanism for amino acid formation, for peptide formation, for RNA formation on a peptide. Again, arguments from analogy fail when the analogies are not closely related. These situations are not closely related. I'm afraid that I must reject your analogy.

 

[Dave1001]

I know you like to imagine you're scoring rhetorical jabs with your subtle wit over there, but your complete incoherence makes whatever point you're trying to make impotent.

Here in reality, I'm afraid we'll have to agree that you're wrong. We're in a thread right now talking about creationists and with creationists. Do you have a problem with my pointing out a flaw in their approach?

No, I have a problem with people who in discussing a hypothesis, contrast it with something weaker than the strongest arguments against it (such as arguing for a specific hypothesis of abiogenesis by contrasting it with biblical creationist theories). It's a waste of collective energy, in my opinion. I disapprove.

 

[RecoveringYuppy]

Interesting that according to this article it [tremendous numbers of viruses in seawater] was only verified about 20 years ago. Well, intuitively I think this information helps the abiogenesis argument quite a bit, because the more viruses out there interacting, the more opportunity for replicating cellular life to emerge in part from them, it seems to me.

Well, it drives home the idea that there is continuum between life and non life on Earth right now. But we don't know if the viruses preceeded the bacteria. The strands of RNA/DNA could be from the break down of bacteria, plasmids or other lifeforms.

 

[kjkent1]

I'm sorry but... We use statistics to calculate likelihoods all the time, on events that have already occured. Sure it is P=1.0 after the fact, but at some time in the past it was not.

It's funny you say "The answer is unequivocally, Yes. In our universe, this incredible accident actually occurred -- accomplished not by one million monkeys, but by only ONE! His name, of course, was William Shakespeare."

In a debate on "design", perhaps you'd be dismissed for having uttered a blunder of the first kind. Shakespeare is an intelligent designer.

Question: Is quantum uncertainty a real phenomenon, or an illusion?

 

[delphi_ote]

No, I have a problem with people who in discussing a hypothesis, contrast it with something weaker than the strongest arguments against it (such as arguing for a specific hypothesis of abiogenesis by contrasting it with biblical creationist theories). It's a waste of collective energy, in my opinion. I disapprove.

You know, I might have a problem when unicorns pooping in my breakfast cereal, but I think it's a waste of collective energy to rant about something I invented out of thin air.

Life at some point came from non-life. That is not one specific hypothesis of abiogeneis. That's the definition of the word.

 

[Skeptic Ginger]

If Mike is accused of murder and the detective says he is guilty, the detective will have to show how Mike might have gotten to the crime scene. But Mike's lawyer says Mike was a thousand miles away an hour before the crime but has no alibi for the crime itself. The detective says "we don't know what processes occured that could have acted as [means for Mike to have gotten to the crime scene and back to where he was in a short period of time.]" (note the quote is partially from what you said about abiogenesis).

I'm acting as Mike's lawyer, showing that, with the gap of evidence that shows how Mike could have gotten to the crime scene, he would have had to travel faster than the speed of sound. The detective says "it is possible to travel faster than the speed of sound". The detective is on better ground showing Mike is guilty than we are in showing that abiogenesis could have happened by chance aided by some autocatalytic mechanism that springs also from chance.

When it comes to abiogenesis, we only have hypotheses like autocatalytic sets. No one knows how simple or complex the minimum autocatalytic system needs to be.

You agree we haven't enough theory on this and I agree. So I calculate the probability to jump a gap much much smaller than from amino acids to DNA (or RNA of equal size or protein of equal size). A sequence of 400 symbols, 4 in a set, is a huge leap. Everyone should do some calculations like this to put this in perspective for themselves. What they conclude from it is up to them.

Argument by false analogy doesn't cut it here. We understand how one travels 1,000 miles and we know the current time constraints on that travel.

We know a lot about the conditions life might have formed under, but there is no certainty of evidence there. There are so many possibilities given what we observe just in our own solar system. Four billion years ago, what we have to go on determining the exact conditions on Earth, determining all the different conditions possible in different locations on the Earth, to make the claim you see an impossibility in the equation is naive at best.

 

[Skeptic Ginger]

Crick may or may not have had an issue about the timing from the early Earth to when life arose...

Crick and Orgel suggested that Directed Panspermia might help resolve some mysteries about life's biochemistry. For instance, it could be the reason why the biological systems of Earth are dependent on molybdenum, when the chemically similar metals chromium and nickel are far more abundant. They suggested that the seeds for life on Earth could have originated from a location far richer in molybdenum.

Other scientists have noted, however, that in seawater molybdenum is more abundant than either chromium or nickel.

Coming full circle to his groundbreaking discovery of DNA's structure, Crick wondered, if life began in the great "primeval soup" suggested by the Miller/Urey experiment, why there wouldn't be a multitude of genetic materials among the different life forms. Instead, all life on Earth shares the same basic DNA structure.

But from this summary it appears Crick's reasoning was also or rather because there wasn't a multitude of genetic materials among different life forms. So Crick favored the panspermia hypothesis.

But it is actually the opposite, if life were raining down on the Earth, we should see multiple genetic lines in the planet's genomes.

Since the conditions are completely different on Earth today than they were 4 billion years ago, that can explain why we don't see a lot of protolife examples. As well life fills the planet so protolife may just not be competitive and disappeared early.

Panspermia is not a well accepted theory due to the fact we seem to have one genetic line. However, organisms exchange a lot of genetic material so more than one initial source could have mixed to become indistinguishable as one line eventually emerged to form multicellular lifeforms.

With the panspermia model you have a couple of problems. We know life can survive in space. It would have to be inside rocks to survive entry into the atmosphere but that is possible. Distance makes it extremely unlikely to have come from other solar systems let alone other galaxies. So if it were common enough to have reached Earth, it would have to have been uncommon enough to not be detected in recovered meteorites. It would have had to be in a form where conditions on the early Earth were favorable. So you start multiplying odds and you get something that is rare, inside a rock, landing on Earth, which just happened to have the just right conditions. It is just more probable life arose here.

Crick didn't not have the advantage we have today of all the genome analyses, (though he did die at 88 in 2004 so he would have seen the information as we acquired it), when he formulated his hypothesis.

It's interesting Creationists love to trot out old science to make their cases.

 

[articulett]

You guys!

No... it WAS Crick.

Crick wrote a book in the early 90's. What was it... "Life Itself" ? I'm not going to look it up right now.

Crick came to doubt evolution could have happened on earth without being previously developed somewhere else. Then he posits that life was directed here, like with spores via interstellar travel of some kind. Kind of like Hoyle and others have mused.

So... YES: Crick!

Francis Crick wrote a book called the Astonishing Hypothesis in 1994 in which he conclude that consciousness in generated by the brain.

 

[articulett]

I
In a debate on "design", perhaps you'd be dismissed for having uttered a blunder of the first kind. Shakespeare is an intelligent designer.

And he evolved from the primordial soup!

Caroline Porco pointed out that there are many teapots circling the sun--they just happen to be attached to the earth and circling the sun with the earth's orbit.

 

[JJM]

Originally Posted by VonNeumann

Crick wrote a book in the early 90's. What was it... "Life Itself" ? I'm not going to look it up right now.

Crick came to doubt evolution could have happened on earth without being previously developed somewhere else. {snip}

Speculation, even from a Nobel Laureate, is still only that- speculation. More importantly, this particular guesswork doesn't change anything. The belief that life started elswhere and came here does not negate any of our evidence for evolution. The ID-creationists like to trot out this inane notion as if it were a non-religious alternative to evolution; when it is clearly in accord with their ideas about god. It only moves the site of "creation." Maybe another planet has better feng shui.

 

[articulett]

What's the deal with people who believe wierd things using analogies in debates? Why can't they just discuss the topic? Anyone else notice this trend?

Von is big on metaphors...he does the Turing machine argument too--

What else is there when the facts aren't on your side.

In the former analogy he's defending someone or other and basically his argument is that if my client did it, it would have to be "magic"-- but he's made some assumptions that only a creationist would make (and a defense lawyer trying to obfuscate...I believe OJ's lawyer's did it -- and Scott Peterson's lawyer's tried--just keep repeating "it couldn't have happened, there wasn't enough time")

It's the kind of thing that you can't really give an answer too, because no matter how you show that there was enough time, it will not register in the creationist mind. It can't. Just like Kleinman's math. They each have their key conundrum that they will never allow to be explained to their satisfaction--it makes them feel like they are fighting and winning points for their invisible judge in the sky.

And I do worry about this wedge strategy. It's a well known tactic to discredit evolution and keep kids stupid--it's dishonest, and I'm sure they have members of the discovery institute out on forums trying to find out what science knows, so they can obfuscate or explain away, with their "god". So I'm getting more like Dawkins, and less willing to indulge this deception.

There is a huge difference between saying "science can't explain this" and actually explaining it better yourself. Creationist never do.

Okay, Von, if there wasn't enough time, what do you imagine happened...and how can we test it to see if it's a valuable learning tool. Because we seem to have gotten pretty damn far on the theory we have.