Sunday, December 21, 2008

The RNA World

Special guest column by Reginald Selkirk:

Many Creationists will point to the complexity of modern biological cells and proclaim that something so complex could not possibly have assembled by pure chance, therefore God (or the unnamed-for-legal-reasons Intelligent Designer) must have done it. Sometimes the argument will be made more specific, such as that N proteins of M residues each must be necessary for a minimally functioning cell, and when you calculate the probability of those proteins appearing together simultaneously, with a 1/20 chance of a particular amino acid residue in each spot of each protein sequence, the odds are astronomical. Or they may point out that proteins are necessary for the replication, transcription and translation of genes, and genes are necessary for encoding proteins, so that there is a chicken or egg circularity to any origin schemes. Such arguments do not point out legitimate weaknesses in evolutionary theory, they only highlight the ignorance of the typical Creationist about matters of biology.

Before we get started on a discussion of the origin of life, let's get the timeframe straight. Current evidence tells us that the age of the universe since the Big Bang is about 13.7 billion years. The age of planet Earth and the solar system is about 4.5 billion years. These dates are supported by several independent fields of science and lines of evidence, including astronomy and radiochemistry. Anyone denying these figures can take their ball and go home right now, because the game they are playing is not science.

The main problems with the "cells are too complex" argument are 1) that it looks at a modern cell, and 2) that naturalistic evolutionary processes are mistakenly perceived as being entirely random.

To tackle the second misconception first, evolution is not entirely random. Variation in organisms due to various forms of mutation or recombination are indeed presumed to be random, but the natural selection which weeds out the failures and allows the successes to flourish is anything but random. To suggest that evolution is entirely random is akin to stating that since any foot race has an element of randomness which might influence the outcome, the Olympic 100 meter dash is equivalent to a lottery. Not so, the participants were selected at many different levels before they even made it to the Olympics. With evolution, the argument is even more absurd, since successful organisms replicate themselves more successfully, and thus have more chances for their offspring to participate in subsequent rounds of competition.

Modern cells are indeed complex. A great deal of the chemistry involved has been worked out in the last century or so. First of all, there is no evidence indicating that the chemistry that takes place within organisms is different than chemistry that takes place outside of cells. Biochemistry has identified most of the metabolites involved, and they conform to known physical and chemical laws. The same sort of reactions occur inside and outside cells. The same atomic theory holds, and the same electron orbital theory. There is no magic ingredient that makes a living thing alive. Chemicals can be synthesized from nonliving sources and introduced into living systems, where they will behave identically with chemically identical biogenic compounds. Much of modern molecular biology consists of using biologically derived catalysts (enzymes) to facilitate reactions outside of living things. Vitalism is dead, and biochemistry killed it.

The Creationist mistake is assuming that modern, complex cells were present at the origin of life. This is analogous to supposing that since cavemen could not construct a modern Mercedes Benz, therefore automobiles cannot have been invented by men, but must have been introduced into modern society by gods or space aliens. (This is an analogy. Analogies are made to illustrate arguments. They should not be stretched too far.) We know that early humans worked their way up through wheelbarrows, carts, chariots, animal-drawn carriages, and early engine-driven carriages before the current incarnations of autos "evolved." In a similar manner, biologists who accept and understand evolution (i.e. almost all of them) believe that early forms of life were much simpler than those we see today, which are the result of billions of years of evolution. Thus, the Creationist argument based on the complexity of modern cells is a straw man fallacy.

Modern cells mostly follow the Central Dogma of Molecular Biology, which proposes that genetic information is stored in DNA, that the information is transcribed into RNA, and then translated into proteins. At the time of the Central Dogma (late 1950s), DNA was viewed as the central repository of information, RNA was viewed as a relatively unimportant go-between. Most of the functional stuff in organisms is done by proteins. Proteins form most of the enzymes which catalyze metabolic reations. Proteins fill structural roles within the cells (microtubules and actin fibers) and outside cells (collagen in ligaments, keratin in skin, crystallin in the lens of your eye). Proteins transport things from here to there (hemoglobin in your red blood cells, ion pores in cell membranes). It is hard to imagine modern cells without proteins. But remember, we're not concerned with modern cells, but with the ancient precursors of modern life, which may even predate the development of cells.

One important exception to the Central Dogma which carries important insights into biological function and history (and shows the lack of respect scientists have for any "dogma") is reverse transcriptase, an enzyme which copies RNA into DNA. RNA (ribonucleic acid) and DNA(deoxyribonucleic acid) are closely related linear polymers which both fall into the general class of nucleic acids. DNA's ability to store and replicate genetic information is based on its ability to form double-stranded helices with base pairing. RNA shares this important property. DNA can form a double helix with DNA, RNA can form a double helix with RNA, and DNA and RNA can form a double helix together. This is how DNA is copied into RNA in cells in order that genes might be read and translated by the ribosomes. Reverse transcriptase is an enzyme which performs the opposite function, it starts with a strand of RNA, and using the double helical base-paring properties of nucleic acids, constructs a complementary DNA chain. In the modern world, reverse transcriptase is used by retroviruses, viruses which transmit their genes as RNA, but which can copy themselves into the DNA genome of the host. Prominent examples of retroviruses include HIV (human immunodeficiency virus) and chicken pox. The discovery of reverse transcriptase allows us to imagine a world without DNA, in which celular genetic information was carried in RNA, as it is in many viruses even today.

As already stated: consistent with evolutionary thinking, biologists propose that early forms of life were simpler than those available for study now. Once the main ingredients of cells were worked out in the middle of the 20th century, people started wondering about which of the major linear biopolymers, DNA, RNA or protein might have come first. RNA was a favorite candidate because not only can it carry and replicate information in the same manner as DNA, but it is more chemically reactive than DNA and could presumably catalyze chemical reactions. The term RNA World was first used by Walter Gilbert in 1986, although others had already made similar suggestions.

Although RNA's theoretical ability to catalyze reactions was known, no examples of RNA catalysts had been identified, and this was a sticking point for the RNA World hypothesis for quite a while. I will digress a bit here and mention that RNA is comparatively difficult to work with in the laboratory. DNA and protein can be extracted from cells without too much difficulty, but RNA is chemically less stable than DNA, and RNase, an enzyme which specifically breaks down RNA, is ubiquitous. It is all over your hands, it is pretty much everywhere. An obvious reason for this is that RNase helps protect you against attack by viruses, many of which carry their genome as RNA. To isolate RNA in the laboratory requires careful technique and the use of chemicals which inhibit the action of RNase.

Francis Crick, famous as one of the discoverers of the DNA double helix, wrote a book on directed panspermia in 1982, Life Itself. Directed panspermia is the idea that aliens deliberately seeded life on earth by sending starting organisms across interstellar space. This does not really answer the question of the origin of life, but it does allow one to push the answer back a few billion years, since the aliens would presumably have to evolve for a few billion years before they reached the technological sophistication necessary to seed other planetary systems. However, one cannot push the origin of life back too far, because astrophysics tells us that the heavy elements which make up much of life ("heavy" means anything heavier than hydrogen and helium to an astrophysicist) were created in early stars. Directed panspermia has a lot of difficulties of its own, and the only reason I mention it is because Crick stated as one motivation for writing his book the fact that no RNA catalysts had been identified at that time.

It wasn't too much longer before the first RNA catalysts were identified, and Thomas Cech and Sidney Altman shared the Nobel Prize in 1989 for those discoveries. RNase P is a piece of RNA which cleaves RNA. These discoveries renewed interest in the RNA World.

What other evidence might exist for the RNA World? First of all, we must adjust our expectations to the question. We are wondering about an environment that existed over 3 billion years ago (possibly closer to 4 billion) and left no macroscopic fossils lying around, as the dinosaurs did. A large portion of the Earth's surface has been recycled over the planet's history by the forces of plate tektonics. Any chemical evidence of the RNA World may have been scavenged by later, more successful life forms to which it gave birth. Modern cellular life has now been identified at deep ocean vents, in polar ice caps, in hot springs, and deep underground. Life is now almost everywhere on our planet, and is even believed to be responsible for creating the oxygen-containing atmosphere which allowed for the evolution of large oxygen-breathing life forms such as ourselves.

One way to deal with this challenge is to look for "molecular fossils" within the cells of modern organism. That is, evidence of our origins may be embedded within the make-up of our own bodies, and within the cells of all living organisms. To summarize briefly, additional RNA enzymes have been identified. DNA raw materials in cells are constructed from RNA raw materials, which points to RNA metabolism as being earlier and more central than DNA metabolism. This conversion is carried out by ribonucleotide reductase, and forms of that enzyme in all known branches of life appear to be homologous (descended from a common origin.) This supports the RNA World, and also suggests that gene-encoded proteins preceded the introduction of DNA to cellular metabolism. More recent speculation supposes that the shift from RNA to DNA as the primary genetic storehouse came about as a result of competition between viruses and their hosts.

The capstone of evidence for the RNA World has come within the last decade from researchers working on ribosomes, the protein-producing factories within cells. Ribosomes have been worked on for quite a while, but they are huge as enzymes go, consisting of dozens of subunits of both RNA and protein. Only around the turn of the century did these huge complexes succumb to the technique of X-ray crystallography, which uncovers the structure of molecules down to the atomic level. And the information uncovered was very exciting: the catalytic core of the ribosome is a ribozyme, i.e. an RNA enzyme. The implications of this for origin of life studies is clear: cellular proteins are manufactured by RNA (with a few odd exceptions), and they always have been. The Creationist charge of chicken:egg::DNA:protein circularity is based in ignorance of biological fact.

The evidence for the RNA World is not as extensive as the evidence for evolution through natural selection, or the evidence for quantum mechanics, but it is solid enough to convince most biologists that it is a sound theory of what an early stage of life on this planet looked like. This still leaves many questions: What was the nature of the RNA World: what, where and when, etc. What came before it? How did we get from there to where we are now? The existence of unanswered questions is not a reason to give up and praise God, it is a reason to do more science, and researchers are doing just exactly that.

If you would like to learn more about current theories on the origin of life, i recommend the book Genesis: The Scientific Quest for Life's Origins by Robert Hazen (ISBN-13: 978-0309103107)

A few web links on the origin of life:

You might notice that most of these links are a few years old, I recycled them from a previous summary. Rest assured that scientific research has continued since then.

EVOLUTION WEB RESOURCES

57 comments:

Larry Moran said...

To suggest that evolution is entirely random is akin to stating that since any foot race has an element of randomness which might influence the outcome, the Olympic 100 meter dash is equivalent to a lottery. Not so, the participants were selected at many different levels before they even made it to the Olympics. With evolution, the argument is even more absurd, since successful organisms replicate themselves more successfully, and thus have more chances for their offspring to participate in subsequent rounds of competition.

On the other hand, saying that evolution is entirely nonrandom is just as bad.

Given that the vast majority of all evolutionary events are due to random genetic drift and not to natural selection, it is very silly to pretend that there's no "randomness" in evolution.

By the way, there's a correct version of the Central Dogma of Molecular Biology and a very incorrect version that has been "refuted" many times.

This posting uses the incorrect, strawman, version. Here's the correct version: The Central Dogma of Molecular Biology.

Reginald Selkirk said...

It is a privilege to be corrected by the best. I have a special interest in the RNA World because my ancestors survived it.

Bror Erickson said...

"The existence of unanswered questions is not a reason to give up and praise God, it is a reason to do more science, and researchers are doing just exactly that."
I take issue with this statement. No one is asking you to give up anything. There are plenty of God believers out there that are constantly researching and adding to the body of knowledge we call science. If you don't want to believe in God don't believe in him. But your reasoning here is curious. However I doubt the microscope will ever give us an answer to whether or not there is a God. Some will look in and see evidence of God's handiwork, and some will look through it and refuse to see it. It is no more going to establish the case than the fact that we are here. And nothing in the microscope is going to give us more reason to praise God than the forgiveness of sins he won for us on the Cross.

Reginald Selkirk said...

However I doubt the microscope will ever give us an answer to whether or not there is a God. Some will look in and see evidence of God's handiwork, and some will look through it and refuse to see it. It is no more going to establish the case than the fact that we are here.

You can fight that fight with the many theists who see evidence for God in the natural world, such as Brigitte.

Eric Sotnak said...

Moderately relevant and relatively non-technical news item:
http://www.sciencedaily.com/releases/2008/12/081218213634.htm

Bror Erickson said...

Reginald,
You write, "You can fight that fight with the many theists who see evidence for God in the natural world, such as Brigitte."
I tend to think that fight needs to be fought on both sides. I tend to think that creation does bear testimony to God. Of course that is inferred by my use of the word creation. However, if one refuses to see it when looking at that which can be seen with the naked eye, I don't know that the microscope is going to be much more effective. Some seem positively scared of the idea of God.
I would posit that there is far less reason to believe Aliens started life on earth, than that God created life. But either way, if you were to go with panspermia, you have admitted intelligent design. Unless you think it was unintelligent life that made space craft and came to earth to begin the origins of life. The God hypothesis has much fewer complications than the ones you admitted with panspermia.

Reginald Selkirk said...

But either way, if you were to go with panspermia, you have admitted intelligent design. Unless you think it was unintelligent life that made space craft and came to earth to begin the origins of life. The God hypothesis has much fewer complications than the ones you admitted with panspermia.

Bore Erickson: please work on your reading comprehension. Two primary panspermia hypotheses have been put forward:

Directed panspermia, as mentioned here, in which aliens seeded life on Earth deliberately. I do not support this hypothesis. The only reason I mentioned it is that Crick cited the failure to identify RNA catalysts as his motivation for writing about this hypothesis. As reported in my essay, and as you should have noticed, this failure has been remedied.

Undirected panspermia, as championed by Fred Hoyle and Chandra Wickramasinghe, in which life first developed in asteroids or comets, which then infected Earth. Hoyle and Wickramasinghe are quick to point out some of the flaws in the directed panspermia hypothesis. Undirected panspermia has its own problems, including a notable vagueness about how exactly life started on said comets or asteroids.

I do not support either of these panspermia hypotheses. The God hypothesis you prefer suffers from the serious shortcoming that there is absolutely no evidence that any such God exists. I also do not accept that hypothesis. I do accept the RNA World theory, based on evidence I cited here.

Bror Erickson said...

"The Creationist mistake is assuming that modern, complex cells were present at the origin of life."
I guess the question here is what evidence do you have that they weren't? Your essay is very informative Reginald, and fairly clear for a none bio chem major like me. However, after the above quoted sentence the word "may" creeps into your essay over and over again, introducing speculation. Speculation is good, especially for science, it leads to new tests, new theories etc. But it is not fact, and it isn't science. And from what I can tell you offer little evidence that supports your speculation, but every conceivable reason is given for the absence of evidence for your hypothesis, the speculation you want to believe in, and want me to believe in.
It was Bo Giertz, who wrote in "Evangelische Glauben" in the 1950's that "For those of us who were born at the turn of the century, the scientific world view has changed at least three times." As well it probably should, dogmatism does not become science, new discoveries should change one's outlook on how the world operates. But when you ask us Christian to give up faith in a creator,based on what may be true you are asking too much. I may not be able to convince you by looking through a microscope, but neither are you going to convince me with speculation. Especially given that I believe in a God who became man for us men and for our salvation, who does not want to judge us, but forgive us, and went so far as to die for us, so that we could live with him. That a man rose from the dead is much easier for me to believe than your speculation and excuses for the absence of evidence backing it up. It also has better evidence. At least until the open up area 52 or what ever the alien believers call it.

Bror Erickson said...

Reginald,
I gathered that you don't like the panspermia hypotheses. I also gathered that you find them more credible than the God hypothesis. Which is what I found curious. Perhaps I read to much into your mention of it.
By the way, it is Bror, not Bore which would be the barrel of a shotgun.

Carlo Sclippa said...

I do not see evolution theory as having any impact upon having faith in God. In fact, evolution theory does a good job of explaining a lot of things about life. Even the book of Enoch we are told that God made regularities in nature. Issac Newton reiterated this notion in his action principle "every action has an opposite and equal reaction". And I also think that the answers that the theory of evolution explains are quite different than answers about the origin of life in the absolute sense. Perhaps God may be hard to prove through evidence. But we also must consider the scope of such a being. Are our minds really capable of perceiving enough of god at a single instance to see him? We humans are still struggling with understanding what constitutes as a whole object through its parts.

P.S. Thank you McCormick for being such a great teacher. In my first semester of graduate work I received an A and a B. I can only think this was largely due to your rigorous paper criticism. You really helped me prepare for graduate work :)

Merry christmas and God bless sir!

Reginald Selkirk said...

The God hypothesis has much fewer complications than the ones you admitted with panspermia.
...
I gathered that you don't like the panspermia hypotheses. I also gathered that you find them more credible than the God hypothesis. Which is what I found curious.


No, I do not favor any panspermia hypothesis I have seen. I consider them to be unlikely, and to lack evidence. However, at least they are scientific hypotheses which could in principle be tested. We could in principle go scouting the galaxy looking for other instances of life, and see if they are compatible with our own. That would be evidence in support of directed panspermia. There is evidence against it, such as the known variation in the genetic code here on Earth. We could travel to the comets and asteroids and search for precursors of life that might support undirected panspermia. We could conceivably find evidence of early life here on Earth, thus providing additional evidence against panspermia.

What evidence might we find that a) gods exist and b) that they created life on Earth? The existence of any supernatural being would be a whopping huge "complication." None of the evidence put forward so far is the least bit compelling, and your standards for judging evidence have been shown to be inconsistent. I.e. you believe what you want to believe, and accept evidence for it, but not evidence against it.

I don't know why you should find it curious that I do not believe that a supernatural being created life. I have expressed it clearly and consistently.

It was Bo Giertz, who wrote in "Evangelische Glauben" in the 1950's that "For those of us who were born at the turn of the century, the scientific world view has changed at least three times."

From which I can distill these truths:

That science does change when presented with new evidence. Religion, not so much.

That the scientific method provides a means of disproving hypotheses, and giving us objective criteria by which to reject one theory in favour of another. Religion, not so much.

That Bo Giertz was fortunate to live in a time when science had largely thrown off the shackles placed on it by religion in earlier times.

Bror Erickson said...

Reginald,
You could test the truth claims of Christianity. There is one test Christianity puts forth, the resurrection from the dead. But then you have to apply the methods of historical investigation to the matter to see whether it happened or not. Or even if it was more likely that it happened, than that it did not happen.
I think it might be a more worth while endeavor for you, than thinking up possible reasons for the lack of evidence to support your current speculation. There is at least evidence for the resurrection.

Bror Erickson said...

"That Bo Giertz was fortunate to live in a time when science had largely thrown off the shackles placed on it by religion in earlier times."
Perhaps, someday science will also throw off the shackles it places on itself. And stop labeling hypothesis as unscientific if they leave open the idea of a God. Yet consider it scientific because it talks about aliens.

Eric Sotnak said...

Bror Erickson wrote:
"There is one test Christianity puts forth, the resurrection from the dead."

This is one of my sticking points with Christianity. What, exactly, is the doctrine? Lutherans recite the Apostle's Creed, which includes belief in 'the resurrection of the body', and the Nicene Creed which contains the line 'I look for the resurrection of the dead'. Nowadays, however, almost no one seems to look for the resurrection of the dead. When Aunt Minnie dies, the kind of thing people say is "She's in Heaven now", even while they are viewing the body at the funeral home. No one says, "Some day she will be resurrected". Where is the resurrection of THE BODY? Most people have gone over to a purely spiritual afterlife, or perhaps a belief in some kind of spiritual/ghost body that exists on some alternate plane. Gone is the belief that one's actual physical body will be resurrected.

But here's a big problem: If it isn't the actual physical body that gets resurrected, then why the insistence that Jesus rose BODILY from the dead? Why was it so important that the tomb be empty? And if Jesus rose bodily from the dead, then all the believers who think that Aunt Minnie is NOW in heaven are wrong, and it seems no one thinks to correct them on that mistake.

Christianity seems positively schizophrenic on the whole life-after-death doctrine to me.

(By the way, Merry Christmas!)

Reginald Selkirk said...


Perhaps, someday science will also throw off the shackles it places on itself. And stop labeling hypothesis as unscientific if they leave open the idea of a God. Yet consider it scientific because it talks about aliens.


Many persons throw off the shackles that science places on itself. That's why so many people believe in astrology, psychic powers, magic, alien abductions, perpetual motion machines, etc. If science itself ever becomes unscientific, our civilization is in deep trouble.

Wandering in a vast forest at night, I have only a faint light to guide me. A stranger appears and says to me: "My friend, you should blow out your candle in order to find your way more clearly." This stranger is a theologian.
- Denis Diderot



Now you're just being silly. I didn't say that directed panspermia was scientific because it talks about aliens. I said it was scientific because it is, at least in principle, testable.

And I don't label hypotheses unscientific if they involve the idea of a God. For example, there have been numerous studies of the medical efficacy of intercessory prayer. These are perfectly scientific. And they all show that intercessory prayer is ineffective. Except for those studies which are fraudulent. So then, we can say that it is scientifically determined that intercessory prayer has no significant effect. We can also establish, with scientific certainty, that people sometimes commit fraud in the name of their religious beliefs.

All such studies make some assumptions about the nature of God. We can test a god who intervenes in the natural world by responding to intercessory prayer, etc. The only difficulty is in extending these conclusions to gods who are untestable and pointless. But since those gods are pointless, who cares about them?

Reginald Selkirk said...

Why was it so important that the tomb be empty?

I never understood the empty tomb argument.

"Look, I have an invisible leprechaun in my hand."

"I don't see anything."

"See? That proves that it is invisible."

Reginald Selkirk said...

You could test the truth claims of Christianity.

Me? But I don't believe in Christianity, and thus have no motivation to convince anyone else that it is true. You could test the truth claims of Christianity. Let's start with Mark 16:17-18:

[17] And these signs shall follow them that believe; In my name shall they cast out devils; they shall speak with new tongues;
[18] They shall take up serpents; and if they drink any deadly thing, it shall not hurt them; they shall lay hands on the sick, and they shall recover.


You can start by drinking poison.

Reginald Selkirk said...

The origin and evolution of the ribosome

Temple F Smith, Jung C Lee, Robin R Gutell, and Hyman Hartman, Biol Direct. 2008; 3: 16.
Published online 2008 April 22. doi: 10.1186/1745-6150-3-16.

Background
The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the two subunits, exploiting the detailed three-dimensional structures of the bacterial and archaeal ribosomes, is especially informative.
...

Matt McCormick said...

I've been thinking about this historical argument and "inerrant word of God" nonsense a lot lately. Here's a glaring problem that's rarely noticed:

Even the names of the Gospels themselves suggest that they can't be trusted as reliable historical documents. They weren't written by the disciples Matthew, Mark, Luke, and John. But the view that they were has been actively propagated by believers in order to foster the illusion that the case for Jesus is better than it is. If the names of the documents are a deliberate deception, then how seriously can we take the claim that what they say is to be trusted.

Then, even if we do take the content seriously, the problems are too numerous to count. Here's what's revealed when we treat the early Christian documents as historical sources:

Did the Believers Believe?

Putting the Fox In Charge of the Henhouse

Perfect Word of God? Reliable Historical Document?

Should We Believe that Jesus Was Resurrected?

Grave Robbers or Magic

300 Year Gap

You Don’t Really Believe in Miracles

Bror Erickson said...

Eric Sotnak,
you write "But here's a big problem: If it isn't the actual physical body that gets resurrected, then why the insistence that Jesus rose BODILY from the dead? Why was it so important that the tomb be empty? And if Jesus rose bodily from the dead, then all the believers who think that Aunt Minnie is NOW in heaven are wrong, and it seems no one thinks to correct them on that mistake.

Christianity seems positively schizophrenic on the whole life-after-death doctrine to me."
The text that most clearly puts forward the doctrine of the resurrection of the dead is 1 Cor. 15. Based on this we Christians believe that we will be raised on the last day in our bodies, just as Christ was raised from the dead in the flesh.
However the Bible is quite silent about the in between state, and many different theories have been put forward. I happen to think that there is a difference between time and eternity. Some believe we go to heaven without out bodies, to be reunited with our bodies on the last day. Others that we sleep until then. But the basic is Christ went to heaven in his Body, and we will live there bodily also.

Matt McCormick said...

Some questions I've always had about how this Christian-zombies-back-from-the-dead story:

There are a staggering number of atoms in the body. After death, those atoms get widely disseminated. It is not improbable, for example, that some of the atoms that were in Shakespeare’s body are in yours. And he got many of his from other people.

So if humans are all resurrected from the grave, who gets the atoms? The first owner? The last owner? What about everyone else in between? Furthermore, the atoms in your body are being regularly discarded and replaced with new ones throughout your life. Which ones get reconstituted in your resurrection?

Suppose in the resurrection it is not necessary to use exactly the same atoms. Instead, all that is needed is to replace carbon with carbon, oxygen with oxygen, and so on. Here’s another difficult question: which body of all the bodies that you have had from birth to old age, and which configuration of atoms gets resurrected? Do you come back as the aging, rapidly failing senior citizen you were the moment before your death? Would eternity in that state be the ultimate reward (or punishment?)

Are you resurrected as a newborn? Once you are resurrected, do you start to age again? Do you age and die, or does your body stay static? If it stays static, do your thoughts change, does your personality mature and grow as it did in your first life? Or are you made into a complete, perfect, unchanging, new being? If so, that would be resurrecting a person who is radically different from the one you are now. How could that complete, static, perfect, new being be you at all if your consciousness and your personality with all the imperfections and limitations that make you unique no longer exist?

Eric Sotnak said...

Bror Erickson wrote:
"Some believe we go to heaven without out bodies, to be reunited with our bodies on the last day."

Then why do we need them?

Also:
"Christ went to heaven in his Body, and we will live there bodily also."

So heaven is a physical place? Made up of atoms, electrons, etc.? Do the same laws of physics apply? Does the matter in Heaven decay, then? Where is Heaven located, since it is a physical place? What is the source of physical energy in Heaven? IS there a sun? What happens when the sun of Heaven burns out?

I suspect the only answer is going to be: "God takes care of all that stuff by magic".

Do you see why I am skeptical, here? It seems that whenever the theist is really pressed to provide details, the answer keeps turning out to be "God does it by magic".

Bror Erickson said...

Matt,
If you had ever bothered to read the primary source materials, namely the New Testament, of the movement you are trying to fight you would realize that there are ready answers for your silly questions. Patton defeated Rommel by reading his book on tank maneuvers. Perhaps you could take a lesson from him.

Bror Erickson said...

Eric,
man was created body and soul, and is never complete without both. I suppose that is why we need them. As for heaven Scripture often portrays it as a recreation of the heavens and earth God created in the beginning. And in a world that has largely accepted Einstein I don't think we need to bicker about the wheres and hows of all this. I'm not an expert in all that, but after watching a nova special on String theory, I see no reason to not believe in heaven, when so many scientists believe in parallel universes etc. Perhaps heaven is one.
I for one find it much easier to believe in the resurrection of the dead, than the spontaneous combustion of life, or this RNA theory that spends half its time explaining why there isn't any evidence for it.

Reginald Selkirk said...

Bror Erickson does not believe in the accuracy of the texts he cites as evidence for Jesus' resurrection.

Bror Erickson said...

Really Reginald I don't? What makes you think so?

Reginald Selkirk said...

You're not willing to take poison in the belief that it will not harm you.

Matt McCormick said...

"If you had ever bothered to read the primary source materials, namely the New Testament, of the movement you are trying to fight you would realize that there are ready answers for your silly questions. "

I've read it very carefully and many times, but I can't find any clear answers to any of the questions that Eric or I have asked. And apparently, since the opinions about the right answers to them are so incredibly varied in the Bible believer community, there aren't any. But let me guess: you think that the Bible clearly and unequivocally supports your and only your account of the afterlife and all of those other Christians who disagree are wrong? If we would all just read it the way you do and study it as much as you do, all doctrinal disputes between the 3,000+ bitterly divided Christian sects would just evaporate? We've heard that from the representatives of all the other sects too. And even within those traditions they have different views. You'd think an omniscient, all powerful God would be a better writer.

MM

Eric Sotnak said...

Bror Erickson wrote:
"after watching a nova special on String theory, I see no reason to not believe in heaven, when so many scientists believe in parallel universes etc. Perhaps heaven is one.
I for one find it much easier to believe in the resurrection of the dead, than the spontaneous combustion of life, or this RNA theory that spends half its time explaining why there isn't any evidence for it."

It seems that you are willing to accept scientific hypotheses when they support your religious beliefs, but not when they don't. That seems to be a case of cherry-picking your evidence, to me.

The RNA World theory, at least, doesn't attempt to fill in gaps by appealing to divine magic. When a scientific hypothesis omits details, its proponents attempt to fill them in by conducting more research. When a religious hypothesis omits details, its proponents fill them in by suggesting that God did it by magic. When Jesus came back from the dead (assuming it did happen), what happened to the cells in his body that had started to decay? Answer: Magic!

Brigitte said...

I've tried to read a little on the RNA world. I can't say that it is more than fuzzy to me at this point. I'll keep my eyes open. (Reginald will be happy to know that I never taught Biology, only Physics.)

I did think about this over Christmas: this and that hypothesis aside, the belief in a Maker of the universe is not really falsifiable and therefore, perhaps, in the end never properly "scientific". This does not make science that is carried on in the name of demonstrating design "unscientific".

If you were an ancient and you believed in the supernatural for some very primitive reasons, those were good reasons for you (sunsets, thunder...). When science started to explain some of these chains of events, it does not change anything, because you can marvel just as much at the parts of this chain. As things become more intricate and the explanations become more sophisticated, you can marvel at all that they explain. You either perceive something more than the sum of the parts,-- or not.

For example, my much admired protein molecules and the incredible cellular machinery, at some point might have been someone's explanation that everything is science and natural explanations and God is not needed to design it. It tells me the opposite.

If you find some super elegant RNA world that explains how things were even earlier, then I will still probably honestly be marveling at the neat mechanism.

--And-- there is so much more to life than the physical aspect of it. I was thinking about how in the beginning there was the LOGOS. That's a big subject and I am not a good enough theologian to explain it well enough.

But there is Logos all the time, the Word, the Intelligence, the Reason you admire, the interpersonal connection between sentient beings, and of course care, love and mercy. The physical supports everything that matters, which may be mind/spirit/information/love. One is pretty much nothing without the other.

This is also, why God became man, and why there will be a physical resurrection of whatever kind. The physical is good and there will always be a place for it. Science is good, too, and there is a place for it. Science and theology can be intricately interwoven and both be true(as we know not for dear Dawkins; but let him rant.).

Bryan Goodrich said...

Bror, you said:

I'm not an expert in all that, but after watching a nova special on String theory, I see no reason to not believe in heaven, when so many scientists believe in parallel universes etc. Perhaps heaven is one.

You seem to have taken away from this video, probably "The Elegant Universe" with Brian Greene, that scientists believe in the multitude of things presented in the video. That would be a very poor interpretation of the facts. Most scientists (physicists) do not believe in string theory. In fact, most professors of physics I've talked to scoff at it. Even in intellectual circles physicists will scoff at it, such as Lisi did at ted.com (link).

What The Elegant Universe (or any such video) presents is a "what if" scenario. If we consider what is possible under the theory, then such and such things would be true. If the theory has an accurate (real) model of reality, then the things it suggests would also be real. That would require scientific investigation and experimentation that doesn't exist. String theory is something talked about in theoretical physics.

With that said, taking that IF the theory were true THEN parallel universes of the kind they talk about (e.g., branes) would be real. Does that mean heaven could be one of them?

That would be a non sequitur since the theory posits certain entities, but there is no basis that the theory begets entities like heaven, angels or gods. Yet, that is precisely the kind of interpretation you provided because you felt like interpreting it that way. Even if string theory is a joke, it is a logical one with a strong mathematical backing. But that only tells us it is a consistent theory which may have nothing to do with reality. Heaven does not have such support, and your interpretation is just hogwash.

Reginald Selkirk said...

For example, my much admired protein molecules and the incredible cellular machinery, at some point might have been someone's explanation that everything is science and natural explanations and God is not needed to design it. It tells me the opposite.

If you find some super elegant RNA world that explains how things were even earlier, then I will still probably honestly be marveling at the neat mechanism.


Translation: Previously Brigitte claimed there was scientific evidence of God. Now she says it's not about evidence, and she will continue to believe in spite of it.

Bror Erickson said...

"It seems that you are willing to accept scientific hypotheses when they support your religious beliefs, but not when they don't. That seems to be a case of cherry-picking your evidence, to me."
I accept a lot of science that has nothing to do with my faith also. But I don't know that I accept string theory or not. I'm just wondering if you make as much fun of parallel universes as you do in the belief in heaven?

Bror Erickson said...

Reginald,
How would you know if I drank the poison or not? I'll let you know that I have not, your inductive reasoning has led you right this time. But the passage of which you speak has its fulfillment in the ministry of the Apostles, Paul being bit by a snake after shipwreck etc. And I stand with Jesus in that whole not testing God thing. If you want to attack a religion learn what it believes.

Brigitte said...

For example, my much admired protein molecules and the incredible cellular machinery, at some point might have been someone's explanation that everything is science and natural explanations and God is not needed to design it. It tells me the opposite.

If you find some super elegant RNA world that explains how things were even earlier, then I will still probably honestly be marveling at the neat mechanism.



... I would be likely marveling at THAT mechanism, is what I meant. The issue remains the same, it just gets moved to different arenas.

Matt McCormick said...

The point, which you seem to be missing Brigitte (and that you should have learned in all of your advanced molecular biology classes), is that as we go back in evolutionary history we explain each stage in simpler and simpler parts, reducing the complication of the mechanism and removing the illusion of purposeful design. So when we explain DNA in terms of RNA, and then RNA in terms of simpler chemical processes, there is LESS to marvel at, not more. Marveling at the remarkable complexity or good fit of parts in the whole is only fitting if you presuppose that the whole completed thing was designed.

It really is obvious that you've switched from trying to give empirical evidence for design on the basis of molecular complexity to just insisting that you'll be amazed at God's creation no matter what the alternative scientific explanation is.

MM

Eric Sotnak said...

Bror Erickson wrote:
"I'm just wondering if you make as much fun of parallel universes as you do in the belief in heaven?"

Hmm.. first off, I don't think I made fun of the belief in heaven. Rather, I stated some reasons why such a belief is problematic.

Consider another problem: On your view, one's physical body is brought back (by magic) from a state of decay and dissolution. How do all the physical constituents of one's body get transported to wherever Heaven is? Again, the only answer I suspect you can offer is: "By magic".

So again you should detect a theme here. I am skeptical of a great many theistic claims because the only way of explaining those claims is by appealing to magic. And I don't happen to find that much of an explanation at all.

But if you can offer alternate explanations that DON'T appeal to magic, I'm willing to listen.

Reginald Selkirk said...

I'm just wondering if you make as much fun of parallel universes as you do in the belief in heaven?

When believers in parallel universes start insisting that I live my life according their beliefs, refrain from publicly mocking them, and use governmental power to enforce those insistences, then I will take your analogy seriously.

Brigitte said...

Matt, I understand what you are saying, but I'm not educated enough at this point to evaluate the RNA theory. And yes, not in spite of, but on top of everything empirical, there are conclusions that cannot be strictly empirical. There is more than what can be measured.

So, you think, to be consistent I HAVE to argue against RNA world?

Reginald, I found this list of implausibilities of the RNA world
here: http://www.answersingenesis.org/home/area/Tools/Quotes/cairns-smith_RNA.asp

I posted them on my blog, too. You can write about it there, if you want. Or are all these objections completely outdated due to discovery of reverse transcriptase?

Brigitte said...

Sorry, guys, I'm in process. I see now that reverse transcriptase has nothing to do with the plausibility of getting polynucleotides in primordial waters.

It's great that RNA can make proteins. BUT we still have no evidence for an RNA world, per se,-- or are all the listed implausibilities thrown over by current research? How do you reasonably get any RNA floating around making protein?

Reginald Selkirk said...

It's great that RNA can make proteins. BUT we still have no evidence for an RNA world, per se,--


Yes, there is evidence. Some of it was presented above.

Reginald Selkirk said...

Reginald, I found this list of implausibilities of the RNA world
here: http://www.answersingenesis.org/home/area/Tools/Quotes/cairns-smith_RNA.asp
...

or are all the listed implausibilities thrown over by current research? How do you reasonably get any RNA floating around making protein?


Answers in Genesis? Those are the people who run the Creation Museum. You could start by finding some better resources. Frankly it's shocking that someone who claims to be a science teacher cannot figure out where to look for up-to-date, accurate information.

I provided quite a few resources above. Have you looked into any of them? The book by Robert Hazen would probably be most relevant, as it is a fairly recent (2005) and it is a broad-ranging overview of the origins of life field by a leading researcher. It should be fairly accessible to non-specialists.

Your link is to a Creationist site discussing an article by A.G. Cairns-Smith which was published in 1982. Yes, that is a bit dated. The discussion itself is not signed or dated; possibly it is by Dean Kenyon. The author provides a list of 19 obstacles to acceptance of the RNA World theory.

I have read Cairns-Smith's book Seven Clues to the Origin of Life, which I found interesting, but it was published in 1985, so it too is dated. He happens to favor a role for clay.

I consider the biological evidence of a central role for RNA in ribozymes, ribosomes, and elsewhere (I didn't even mention enzymatic cofactors) to be convincing evidence that the RNA World actually existed, and that some remnant of it continues in every modern cell. As I already stated, most biologists accept the RNA World theory. Since there is evidence that this actually did occur, I am not particularly swayed by arguments as to the improbability that it did not.

The list of difficulties mostly address the chemical plausibility of getting to an RNA World. These can be countered in a number of ways. Some counter-arguments are linked above in my original post. Points off for you for any argument I have to repeat. It gives the impression you're just not paying attention.

This one is a repeat:
Researchers Study Formation Of Chemical Precursors to Life
In just two years of work, an international research team has discovered eight new complex, biologically-significant molecules in interstellar space using the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) in West Virginia.

"This is a feat unprecedented in the 35-year history of searching for complex molecules in space and suggests that a universal prebiotic chemistry is at work," said Jan M. Hollis of the NASA Goddard Space Flight Center, leader of the research team.

The new discoveries are helping scientists unlock the secrets of how the molecular precursors to life can form in the giant clouds of gas and dust in which stars and planets are born...


These precursors are so abundant that interstellar clouds of them can be identified spectroscopically from a distance of several hundred light years.

Along the same lines:
The Varieties of Scientific Experience, by Carl Sagan (published post-humously in 2006). As a planetary scientist, Sagan was aware of the huge amount of organic gunk that exists in comets, asteroids, and on the surface of planets and moons that have stable surfaces. There's an awful lot of this crud, and it presumably includes a large number of different organic molecules.

The exact composition of the early Earth's surface is not precisely known. This means that the yea-sayers are speculating. But it also means that the nay-sayers are speculating just as much.

Even the concentration of oxygen in the early atmosphere is still under active scientific debate. It is known to have been low, but just how low? Would it have interfered with various proposed reactions?

As for the plausibility of certain molecules forming, I think objections are premature. Most of the discussion is about the original Urey-Miler experiments, and follow-ups to them. In these experiments a small number of chemicals (ammonia, carbon dioxide, etc) are sealed in a container, which is then subjected to electrical arcing, or some such. Variations in ingredients and conditions are still producing new findings.

Did Life Evolve in Ice?
2008

New Results from a 1953 Experiment Offer Hints to the Origin of Life
2008

Devastating Meteorite Strikes May Have Created Earth’s First Organic Molecules
2008

Primordial Soup's On: Scientists Repeat Evolution's Most Famous Experiment
2007

How and Where Did Life on Earth Arise?
2005

The origin of Earthly life is not something that happened in a carefully controlled flask. Imagine a laboratory the size of a planet, with an amazing variety of different environments in which unregulated chemistry was happening: warm puddles, yes, but also hot smoker vents, pyrrhite chimneys, geysers, deep underground, possibly ice packs (Incidentally, all environments in which modern cellular life is know known to thrive). The wide-openness of the question favors the yea-sayers.

----
To switch gears, here's a couple fairly recent things about the plausibility of RNA replication:

Origin Of Life On Earth: Simple Fusion To Jump-start Evolution
Points off: already posted by Eric Sotnak.

Self-correcting messages
Mistakes can occur as RNA polymerase copies DNA into transcripts. A proofreading mechanism that removes the incorrect RNA is triggered by the erroneous RNA itself.
2006

-----------------------

Meanwhile let's consider the evidence for alternative hypotheses:

No fossil skeletons of angels have been found in the fossil record. Absolutely none.

Reginald Selkirk said...

Heard on NPR's All Things Considered, January 8, 2009:

In Lab, Clues To How Life Began
(audio, 4:05)

A report on research published in this week's Science magazine:
Self-Sustained Replication of an RNA Enzyme
Tracey A. Lincoln and Gerald F. Joyce
Science DOI: 10.1126/science.1167856

Brigitte said...

Dear Reginald: thank you for your patient response (and the generous marking scheme! :)

I wrote before that my internet was not accessible most of the holidays. (small outfit via cell phone tower).

I also buried my son this week (18 years old).-- I sure hope there is more to life than molecules.

I will try to get through my reading assignments as time allows.


"No fossil skeletons of angels have been found in the fossil record. Absolutely none."

Writing things like these make you look ridiculous not credibly scientific, academic, Reginald. Marks off.

Reginald Selkirk said...

Writing things like these make you look ridiculous not credibly scientific, academic, Reginald. Marks off.

If you know of fossil, or other credible scientific evidence of angels, please share. Or any other positive evidence of how an Intelligent Designer might have designed - and implemented - the natural world. Otherwise you may understand that at this stage I am not at all impressed with your ideas about what is and is not credibly scientific.

At least when I show some attitude, there is substance behind it.

Brigitte said...

"If you know of fossil, or other credible scientific evidence of angels, please share."

Ah, yes, I forgot, angels are the missing link.

Reginald Selkirk said...

Talk.Origins, one of the most comprehensive Internet archives of information on evolution and creationism, is back in action.

Another book I can recommend is The Emergence of Life on Earth by Iris Fry (2000, Rutgers University Press). It gives a more historical view of the inquiry into the origin of life than the Robert Hazen book, but is a few years older, longer, and somewhat dry.

If you want to see a recent negative outlook from a scientifically respectable source, see A Simpler Origin of Life by Robert Shapiro, Scientific American, February 12, 2007.
The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. Energy-driven networks of small molecules afford better odds as the initiators of life.
While Shapiro questions the RNA World scenario, he does not go in for Intelligent Design, but instead favors a scientific theory called "metabolism-first." By the way, the mischaracterization of opposing theories with terms like "sudden appearance" is one reason I do not agree with Shapiro.

Reginald Selkirk said...

Writing things like these make you look ridiculous not credibly scientific, academic, Reginald. Marks off.
...
Ah, yes, I forgot, angels are the missing link.


This would leave you to explain why you consider my remark about angel fossils to be ridiculous. There are several possibilities.

1) You are aware that there actually are angel skeleton fossils, and you can provide a reference for that information.

2) You know that angels do not leave fossils, and your evidence for concluding this is...

3) You believe that the Intelligent Designer did not use angels when He designed - and implemented - the many facets of the biological world which you attribute to Intelligent Design. Your evidence for believing this is...


You might notice a common factor here. While you seem to consider angel fossils to be ridiculous, you have not proposed any alternative hypothesis to compete with my offerings, and you have not supplied any evidence whatsoever either for why you should feel justified in doubting the prevailing scientific view, or in support of the alternative view you have not bothered to offer.

Since you are concerned with what is "credibly scientific," these omissions must cause you great concern, and you must feel a like a hypocrite suggesting that someone else is not "credibly scientific" when you yourself are not dealing in hypotheses and evidence.

Brigitte said...

Reginald, YOU WIN. There are no angel fossils and there never will be and I can't find you any.

One: nobody every said that they are made of anything with molecules.

Two: they would have had to be crushed in the special conditions needed to form fossils (highly unlikely, if they had any sense to protect themselves). :)

Reginald Selkirk said...

One: nobody every said that they are made of anything with molecules.

Nobody said that, and nobody said the opposite*. The very lack of hypotheses and evidence is my point.


* Actually, in the Bible, angels are visible and audible to people, and so must have some interaction with the Biblical world.

Reginald Selkirk said...

Oops. I meant to write "and so must have some interaction with the material world."

Reginald Selkirk said...

A hierarchical model for evolution of 23S ribosomal RNA
Konstantin Bokov & Sergey V. Steinberg
Nature 457, 977-980 (19 February 2009) | doi:10.1038/nature07749

The emergence of the ribosome constituted a pivotal step in the evolution of life. This event happened nearly four billion years ago, and any traces of early stages of ribosome evolution are generally thought to have completely eroded away. Surprisingly, a detailed analysis of the structure of the modern ribosome reveals a concerted and modular scheme of its early evolution.
...

Reginald Selkirk said...

Chemist Shows How RNA Can Be the Starting Point for Life
By NICHOLAS WADE
Published: May 13, 2009 (NYTimes)

An English chemist has found the hidden gateway to the RNA world, the chemical milieu from which the first forms of life are thought to have emerged on earth some 3.8 billion years ago.

He has solved a problem that for 20 years has thwarted researchers trying to understand the origin of life — how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth. The discovery, if correct, should set researchers on the right track to solving many other mysteries about the origin of life. It will also mean that for the first time a plausible explanation exists for how an information-carrying biological molecule could have emerged through natural processes from chemicals on the primitive earth.
...
In the article in Nature, Dr. Sutherland and his colleagues Matthew W. Powner and BĂ©atrice Gerland report that they have taken the same starting chemicals used by others but have caused them to react in a different order and in different combinations than in previous experiments. they discovered their recipe, which is far from intuitive, after 10 years of working through every possible combination of starting chemicals.
...

Reginald Selkirk said...

Nobel Prize for chemistry of life
The 2009 chemistry Nobel Prize has been awarded to Venkatraman Ramakrishnan, Thomas Steitz and Ada Yonath.

The prize is awarded for the study of the structure and function of the ribosome - the cell's protein factory.

Reginald Selkirk said...

The Times Literary Supplement, Feb 3, 2010
Intelligent Design

Sir, – Stephen C. Meyer and Thomas Nagel are both sceptical of the chemical theory of evolution (Letters, January 15). Nagel suggests no alternative, but Meyer advocates a theory known as Intelligent Design, which proposes that certain features of living things were introduced by a supernatural being at various times in the past. He has also written a book about it. Nagel initially puffed the book using quasi-scientific quotations, but now confesses that he took “the presentation of the data largely on trust”.

The theory of Intelligent Design makes some outlandish claims about DNA and proteins...


STEPHEN FLETCHER
Department of Chemistry, Loughborough University, Ashby Road, Loughborough.

Reginald Selkirk said...

The money paragraph:

In the prologue to his book Signature in the Cell, Stephen Meyer states that it is an attempt to make a comprehensive, interdisciplinary argument for the Intelligent Design view of the origin of life. But as the author himself concedes (in an appendix on page 496), the discovery of a precursor to DNA (such as RNA) would demolish the whole edifice. A “key prediction” is that “Future experiments will continue to show that RNA catalysts lack the capacities necessary to render the RNA world scenario plausible”. It is Stephen Meyer’s bad luck to have published his book in 2009, the very year that the RNA world scenario became eminently plausible. In February of that year came the discovery of the self-sustained replication of an RNA enzyme, by Lincoln and Joyce (Science, Vol 323, pp1,229–32). In March came the identification of the prebiotic translation apparatus (a dimer of self-folding RNA units) within the contemporary ribosome, by Yonath et al (Nature Proceedings, Posted March 4, 2009). Finally, in May came the discovery of the synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, by Powner et al (Nature, Vol 459, pp239–42). I am afraid that reality has overtaken Meyer’s book and its flawed reasoning.

Reginald Selkirk said...

Life on Earth May Have Had an Icy Start
The cracks in ice could have served as a safe environment — much like a cell — for the first life on Earth to replicate and evolve.

The study adds plausibility to the ‘ RNA World’ hypothesis that argues life began with a single stranded molecule capable of self-replication...