Hey everybody!
Just wonderin' how many Alabamians read this blog. And how many of em live near Montgomery. Because if you do, I've got good news!! There's a brand new group called Mongomery Freethinkers which plans on meeting about once a month (Jan 31st is going to be the very first meeting).
Click here to go to their meetup page.
I'll see you there!
Monday, January 12, 2009
Sunday, January 11, 2009
RNA Replicators Created!!!!
Via Sciencedaily:
One of the most enduring questions is how life could have begun on Earth. Molecules that can make copies of themselves are thought to be crucial to understanding this process as they provide the basis for heritability, a critical characteristic of living systems. New findings could inform biochemical questions about how life began.
Now, a pair of Scripps Research Institute scientists has taken a significant step toward answering that question. The scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely.
The work was recently published in the journal Science.
In the modern world, DNA carries the genetic sequence for advanced organisms, while RNA is dependent on DNA for performing its roles such as building proteins. But one prominent theory about the origins of life, called the RNA World model, postulates that because RNA can function as both a gene and an enzyme, RNA might have come before DNA and protein and acted as the ancestral molecule of life. However, the process of copying a genetic molecule, which is considered a basic qualification for life, appears to be exceedingly complex, involving many proteins and other cellular components.
For years, researchers have wondered whether there might be some simpler way to copy RNA, brought about by the RNA itself. Some tentative steps along this road had previously been taken by the Joyce lab and others, but no one could demonstrate that RNA replication could be self-propagating, that is, result in new copies of RNA that also could copy themselves.
In Vitro Evolution
A few years after Tracey Lincoln arrived at Scripps Research from Jamaica to pursue her Ph.D., she began exploring the RNA-only replication concept along with her advisor, Professor Gerald Joyce, M.D., Ph.D., who is also Dean of the Faculty at Scripps Research. Their work began with a method of forced adaptation known as in vitro evolution. The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.
Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.
Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.
Immortalizing Molecular Information
The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.
"This is the only case outside biology where molecular information has been immortalized," says Joyce.
Not content to stop there, the researchers generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.
The research shows that the system can sustain molecular information, a form of heritability, and give rise to variations of itself in a way akin to Darwinian evolution. So, says Lincoln, "What we have is non-living, but we've been able to show that it has some life-like properties, and that was extremely interesting."
Knocking on the Door of Life
The group is pursuing potential applications of their discovery in the field of molecular diagnostics, but that work is tied to a research paper currently in review, so the researchers can't yet discuss it.
But the main value of the work, according to Joyce, is at the basic research level. "What we've found could be relevant to how life begins, at that key moment when Darwinian evolution starts." He is quick to point out that, while the self-replicating RNA enzyme systems share certain characteristics of life, they are not themselves a form of life.
The historical origin of life can never be recreated precisely, so without a reliable time machine, one must instead address the related question of whether life could ever be created in a laboratory. This could, of course, shed light on what the beginning of life might have looked like, at least in outline. "We're not trying to play back the tape," says Lincoln of their work, "but it might tell us how you go about starting the process of understanding the emergence of life in the lab."
Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. "We're knocking on that door," he says, "But of course we haven't achieved that."
The subunits in the enzymes the team constructed each contain many nucleotides, so they are relatively complex and not something that would have been found floating in the primordial ooze. But, while the building blocks likely would have been simpler, the work does finally show that a simpler form of RNA-based life is at least possible, which should drive further research to explore the RNA World theory of life's origins.
One of the most enduring questions is how life could have begun on Earth. Molecules that can make copies of themselves are thought to be crucial to understanding this process as they provide the basis for heritability, a critical characteristic of living systems. New findings could inform biochemical questions about how life began.
Now, a pair of Scripps Research Institute scientists has taken a significant step toward answering that question. The scientists have synthesized for the first time RNA enzymes that can replicate themselves without the help of any proteins or other cellular components, and the process proceeds indefinitely.
The work was recently published in the journal Science.
In the modern world, DNA carries the genetic sequence for advanced organisms, while RNA is dependent on DNA for performing its roles such as building proteins. But one prominent theory about the origins of life, called the RNA World model, postulates that because RNA can function as both a gene and an enzyme, RNA might have come before DNA and protein and acted as the ancestral molecule of life. However, the process of copying a genetic molecule, which is considered a basic qualification for life, appears to be exceedingly complex, involving many proteins and other cellular components.
For years, researchers have wondered whether there might be some simpler way to copy RNA, brought about by the RNA itself. Some tentative steps along this road had previously been taken by the Joyce lab and others, but no one could demonstrate that RNA replication could be self-propagating, that is, result in new copies of RNA that also could copy themselves.
In Vitro Evolution
A few years after Tracey Lincoln arrived at Scripps Research from Jamaica to pursue her Ph.D., she began exploring the RNA-only replication concept along with her advisor, Professor Gerald Joyce, M.D., Ph.D., who is also Dean of the Faculty at Scripps Research. Their work began with a method of forced adaptation known as in vitro evolution. The goal was to take one of the RNA enzymes already developed in the lab that could perform the basic chemistry of replication, and improve it to the point that it could drive efficient, perpetual self-replication.
Lincoln synthesized in the laboratory a large population of variants of the RNA enzyme that would be challenged to do the job, and carried out a test-tube evolution procedure to obtain those variants that were most adept at joining together pieces of RNA.
Ultimately, this process enabled the team to isolate an evolved version of the original enzyme that is a very efficient replicator, something that many research groups, including Joyce's, had struggled for years to obtain. The improved enzyme fulfilled the primary goal of being able to undergo perpetual replication. "It kind of blew me away," says Lincoln.
Immortalizing Molecular Information
The replicating system actually involves two enzymes, each composed of two subunits and each functioning as a catalyst that assembles the other. The replication process is cyclic, in that the first enzyme binds the two subunits that comprise the second enzyme and joins them to make a new copy of the second enzyme; while the second enzyme similarly binds and joins the two subunits that comprise the first enzyme. In this way the two enzymes assemble each other — what is termed cross-replication. To make the process proceed indefinitely requires only a small starting amount of the two enzymes and a steady supply of the subunits.
"This is the only case outside biology where molecular information has been immortalized," says Joyce.
Not content to stop there, the researchers generated a variety of enzyme pairs with similar capabilities. They mixed 12 different cross-replicating pairs, together with all of their constituent subunits, and allowed them to compete in a molecular test of survival of the fittest. Most of the time the replicating enzymes would breed true, but on occasion an enzyme would make a mistake by binding one of the subunits from one of the other replicating enzymes. When such "mutations" occurred, the resulting recombinant enzymes also were capable of sustained replication, with the most fit replicators growing in number to dominate the mixture. "To me that's actually the biggest result," says Joyce.
The research shows that the system can sustain molecular information, a form of heritability, and give rise to variations of itself in a way akin to Darwinian evolution. So, says Lincoln, "What we have is non-living, but we've been able to show that it has some life-like properties, and that was extremely interesting."
Knocking on the Door of Life
The group is pursuing potential applications of their discovery in the field of molecular diagnostics, but that work is tied to a research paper currently in review, so the researchers can't yet discuss it.
But the main value of the work, according to Joyce, is at the basic research level. "What we've found could be relevant to how life begins, at that key moment when Darwinian evolution starts." He is quick to point out that, while the self-replicating RNA enzyme systems share certain characteristics of life, they are not themselves a form of life.
The historical origin of life can never be recreated precisely, so without a reliable time machine, one must instead address the related question of whether life could ever be created in a laboratory. This could, of course, shed light on what the beginning of life might have looked like, at least in outline. "We're not trying to play back the tape," says Lincoln of their work, "but it might tell us how you go about starting the process of understanding the emergence of life in the lab."
Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. "We're knocking on that door," he says, "But of course we haven't achieved that."
The subunits in the enzymes the team constructed each contain many nucleotides, so they are relatively complex and not something that would have been found floating in the primordial ooze. But, while the building blocks likely would have been simpler, the work does finally show that a simpler form of RNA-based life is at least possible, which should drive further research to explore the RNA World theory of life's origins.
Saturday, January 10, 2009
Octopus-capades
You must read this article - It is about octopi who escape from their tanks at the aquarium.
Smart little buggers, they are. Makes me wonder if their consciousness is near human-level (or beyond?!?)
Smart little buggers, they are. Makes me wonder if their consciousness is near human-level (or beyond?!?)
Friday, January 9, 2009
Old Pizza
I have been doing lots and lots of reading lately. I think I've checked out about 20 books from my library in the past few weeks, and I have been reading articles (journal and magazine) galore. It's all so that I can be as informed as possible for the writing of my book (I'm currently working on a draft of the third chapter).
Anyway, I'm now reading an antievolutionary classic. It's Evolution: A Theory in Crisis by Michael Denton.
I found it eerie to read his descriptions of the bacterial flagellum and cilium and his comments on how complex they were. This book totally got the Intelligent Design movement up and running.
Denton also tries to replace the evolutionary understanding of animals' relationships with "typology". The idea is very similar to the creationist concept of a "kind". The big question is: How does one reconcile the concept of distinct "types" with bizarre critters like the platypus? You can't. Denton dodges the issue by pointing out that although marsupials do seem "part mammal part reptile" there is no one part of the animal that seems intermediate, only parts which are fully reptilian or fully reptile. Although this isn't quite true, even if it were true it would be nothing but a red herring. If all animals could be classified into discrete "types" we shouldn't see anything like the monotremes or marsupials.
I suppose the best I could say about the book is that it isn't rude or stupid as most creationist literature is, nor do I get the feeling that Denton is deliberately decieving himself or trying to decieve others. He really believes what he wrote, he is just sorely mistaken.
Anyway, I'm now reading an antievolutionary classic. It's Evolution: A Theory in Crisis by Michael Denton.
I found it eerie to read his descriptions of the bacterial flagellum and cilium and his comments on how complex they were. This book totally got the Intelligent Design movement up and running.
Denton also tries to replace the evolutionary understanding of animals' relationships with "typology". The idea is very similar to the creationist concept of a "kind". The big question is: How does one reconcile the concept of distinct "types" with bizarre critters like the platypus? You can't. Denton dodges the issue by pointing out that although marsupials do seem "part mammal part reptile" there is no one part of the animal that seems intermediate, only parts which are fully reptilian or fully reptile. Although this isn't quite true, even if it were true it would be nothing but a red herring. If all animals could be classified into discrete "types" we shouldn't see anything like the monotremes or marsupials.
I suppose the best I could say about the book is that it isn't rude or stupid as most creationist literature is, nor do I get the feeling that Denton is deliberately decieving himself or trying to decieve others. He really believes what he wrote, he is just sorely mistaken.
Thursday, January 8, 2009
Bill Craig on Pagan Parallels
When they say that Christian beliefs about Jesus are derived from pagan mythology, I think you should laugh. Then look at them wide-eyed and with a big grin, and exclaim, “Do you really believe that?” Act as though you’ve just met a flat earther or Roswell conspirator. You could say something like, “Man, those old theories have been dead for over a hundred years! Where are you getting this stuff?” Tell them this is just sensationalist junk, not serious scholarship. If they persist, then ask them to show you the actual passages narrating the supposed parallel. They’re the ones who are swimming against the scholarly consensus, so make them work hard to save their religion. I think you’ll find that they’ve never even read the primary sources.
-William Lane Craig
Here I have found two gods, one Greek and one Roman, who bear striking similarities to Jesus. I have cited primary sources (translations of the original ancient texts) all of which you can read for yourself via Tufts University’s Perseus Project or through equally reputable University resources.
Romulus
Written about by Titus Livius (who died in 17 CE) in his book “The Early History of Rome” and by Plutarch in “Numa Pompilius”(written circa 75 CE, around the same time Mark’s gospel was written).
The Parallels:Romulus is born of a vestal virgin, which was a priestess of the hearth god Vesta sworn to celibacy (Early History of Rome, 1.3-1.4). His mother claims that the divine impregnated her, yet this is not believed by the King (there is a certain irony to this since Romulus is later hailed as “God and a Son of God”, meaning that his mother’s seemingly far-fetched tale was true after all). Romulus and his twin brother, Remus, are tossed in the river and left for dead (A “slaughter of the innocents” tale which parallels that of Matthew 2:13-16).
Romulus is hailed as the son of god. He is “snatched away to heaven” by a whirlwind (It is assumed that the gods took him), and he makes post mortem appearances (See The Early History of Rome 1.16). In his work Numa Pompilius, Plutarch records that there was a darkness covering the earth before his death (Just as there was during Jesus’ death according to Mark 15:33). He also states that Romulus is to be know afterwards as ‘Quirinus’; A god which belonged to the Archiac Triad (a “triple deity” similar to the concept of the Trinity). This information may be found in the second paragraph of the translation of Numa Pompilius (hyperlinked above).
Heracles (Hercules)
Written about by Diodorus Siculus in the "Library of History" Book 4. Diodorus lived from 90 to 21 BCE (According to his entry in Funk and Wagnall's New Encyclopedia).The Parallels:Heracles is the Son of a god (Zeus).In Library of History 4:9:1-2, it is recorded that Zeus is both the father and great-great- great grandfather of Heracles, just as Jesus is essentially his own grandpa, being both “The root and offspring of David” (Revelation 22:16) as he is part of the triune God which is the father of Adam and eventually of Jesus. Both are doubly related to the Supreme God.
Diodorus writes that,"For as regards the magnitude of the deeds which he accomplished it is generally agreed that Heracles has been handed down as one who surpassed all men of whom memory from the beginning of time has brought down an account; consequently it is a difficult attainment to report each one of his deeds in a worthy manner and to present a record which shall be on a level with labours so great, the magnitude of which won for him the prize of immortality."-Library of History, 4:8:1
Jesus is also said to have done a very large number of good works. John 21:25 says that: "Jesus did many other things as well. If every one of them were written down, I suppose that even the whole world would not have room for the books that would be written."
Hera tries to kill Heracles as an infant by sending two serpents after him (Library of History, 4:10:1) yet Heracles survives by strangling them. This parallels Herod's slaughter of the innocents in an attempt to kill Jesus (Matthew 2:13-16).
Heracles makes a descent into Hades and returns from it with Theseus and Peirithoüs (4.26.1), just as Jesus descends into the “lower parts of the earth” or Hades (Ephesians 4:7-8); Though Jesus does not bring anyone up from it.Heracles' body is not found and he is assumed to have been taken by the gods:"After this, when the companions of Iolaüs came to gather up the bones of Heracles and found not a single bone anywhere, they assumed that, in accordance with the words of the oracle, he had passed from among men into the company of the gods." (Library of History, 4:38:5)
-William Lane Craig
Here I have found two gods, one Greek and one Roman, who bear striking similarities to Jesus. I have cited primary sources (translations of the original ancient texts) all of which you can read for yourself via Tufts University’s Perseus Project or through equally reputable University resources.
Romulus
Written about by Titus Livius (who died in 17 CE) in his book “The Early History of Rome” and by Plutarch in “Numa Pompilius”(written circa 75 CE, around the same time Mark’s gospel was written).
The Parallels:Romulus is born of a vestal virgin, which was a priestess of the hearth god Vesta sworn to celibacy (Early History of Rome, 1.3-1.4). His mother claims that the divine impregnated her, yet this is not believed by the King (there is a certain irony to this since Romulus is later hailed as “God and a Son of God”, meaning that his mother’s seemingly far-fetched tale was true after all). Romulus and his twin brother, Remus, are tossed in the river and left for dead (A “slaughter of the innocents” tale which parallels that of Matthew 2:13-16).
Romulus is hailed as the son of god. He is “snatched away to heaven” by a whirlwind (It is assumed that the gods took him), and he makes post mortem appearances (See The Early History of Rome 1.16). In his work Numa Pompilius, Plutarch records that there was a darkness covering the earth before his death (Just as there was during Jesus’ death according to Mark 15:33). He also states that Romulus is to be know afterwards as ‘Quirinus’; A god which belonged to the Archiac Triad (a “triple deity” similar to the concept of the Trinity). This information may be found in the second paragraph of the translation of Numa Pompilius (hyperlinked above).
Heracles (Hercules)
Written about by Diodorus Siculus in the "Library of History" Book 4. Diodorus lived from 90 to 21 BCE (According to his entry in Funk and Wagnall's New Encyclopedia).The Parallels:Heracles is the Son of a god (Zeus).In Library of History 4:9:1-2, it is recorded that Zeus is both the father and great-great- great grandfather of Heracles, just as Jesus is essentially his own grandpa, being both “The root and offspring of David” (Revelation 22:16) as he is part of the triune God which is the father of Adam and eventually of Jesus. Both are doubly related to the Supreme God.
Diodorus writes that,"For as regards the magnitude of the deeds which he accomplished it is generally agreed that Heracles has been handed down as one who surpassed all men of whom memory from the beginning of time has brought down an account; consequently it is a difficult attainment to report each one of his deeds in a worthy manner and to present a record which shall be on a level with labours so great, the magnitude of which won for him the prize of immortality."-Library of History, 4:8:1
Jesus is also said to have done a very large number of good works. John 21:25 says that: "Jesus did many other things as well. If every one of them were written down, I suppose that even the whole world would not have room for the books that would be written."
Hera tries to kill Heracles as an infant by sending two serpents after him (Library of History, 4:10:1) yet Heracles survives by strangling them. This parallels Herod's slaughter of the innocents in an attempt to kill Jesus (Matthew 2:13-16).
Heracles makes a descent into Hades and returns from it with Theseus and Peirithoüs (4.26.1), just as Jesus descends into the “lower parts of the earth” or Hades (Ephesians 4:7-8); Though Jesus does not bring anyone up from it.Heracles' body is not found and he is assumed to have been taken by the gods:"After this, when the companions of Iolaüs came to gather up the bones of Heracles and found not a single bone anywhere, they assumed that, in accordance with the words of the oracle, he had passed from among men into the company of the gods." (Library of History, 4:38:5)
Principles of Biology II
Yesterday I attended the first class of "Principles of Biology II" over at my college.
It was pretty interesting stuff. We went over the basics: Taxonomy (Three Domains: Eukarya, Prokarya, Archaea, all the way down to the species level of classification), Ecology (how organisms interact with their environments and with each other), and Evolution.
When he was explaining evolution, he said that some people ask, "If Evolution happens then why aren't people born with tails?" His Response: They are. If it happens in India, he told us, they think you're a monkey god. If it happens in the United States, they snip it off at birth and no one says anything about it.
: )
It was pretty interesting stuff. We went over the basics: Taxonomy (Three Domains: Eukarya, Prokarya, Archaea, all the way down to the species level of classification), Ecology (how organisms interact with their environments and with each other), and Evolution.
When he was explaining evolution, he said that some people ask, "If Evolution happens then why aren't people born with tails?" His Response: They are. If it happens in India, he told us, they think you're a monkey god. If it happens in the United States, they snip it off at birth and no one says anything about it.
: )
Wednesday, January 7, 2009
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