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2 comments

Comment the first (0)

damn_registrars (1103043) | about a year ago | (#43236909)

As more schools offer it at the graduate level more of them are recognizing that there are a multitude of paths in that are valid. Hell the last actual bioinformatics group that I worked with myself was, in its final days, led by a guy who did his BS in physics and his PhD in math.

As with so much in life, it's a heuristic problem. In another decade or so, I hope to trundle over to George Mason U, and see about something in Computer Science. The couple of years at GWU were very broadening, and helped make me into the eclectic bag of nonsense I am today.

The tough part about graduate studies - in regards to accessibility for working people - is of course the general requirement of dropping your regular life to work in a lab for little-to-no pay at very long hours for uncertain time. It is rather unfortunate that we don't have a better solution in place for this; I have met PhD students from European countries for example who are essentially employed at biotech companies while doing their PhD research - one would think we could come up with a similar solution here in the states.

If you have a vague interest in it in the future I'd recommend watching out for a conference to come to (or near) your town (the ISMB is especially good, though there are others as well), you can get a taste of who is in the field, what they are doing, and what opportunities might still exist with your existing skills.

Sage advice. What I learned is that I need to pick the doctoral committee, do the Venn diagram of their areas of interest, and work slavishly on something that they kind of know already. All dreams of solving world hunger are for AFTER the degree.

Depending on one's degree choice those dreams are often now scattered out past the first (or even second) post-doctoral position. Many people are finishing their PhD and now finding they need a post-doc position in academia first before industry will talk to them. This situation is of course made more miserable by the lack of funding (and hence lack of hiring) in the academic labs.

although the hypothesis of the RNA world - coupled to the demonstration that RNA can actually perform quite a few enzymatic functions on its own - covers some of it quite well.

So it will be interesting to see if someone can re-create an "RNA world" in a lab, and show that the information can "preciptiate" from RNA to DNA again. Sort of "RAM going to hard drive", to use a wildly inaccurate metaphor.

The analogy is not all that bad, really. After all in life as we currently know it (if, of course, you exclude rna-only viruses and prions [which can reasonably be called not truly alive]) RNA is the transition media and DNA is the long-term storage. Furthermore as best I recall we had digital memory for computers before we had digital storage

That said, showing that RNA->DNA transition spontaneously in an experiment requires either an RNA-dependent DNA-polymerase (RdDp in virology terms) or an error-prone RNA-dependent RNA-polymerase (RdRp), either of which would need to take place in the presence of free DNA nucleotides or with something that would bring about oxidation of RNA nucleotides. The problem is there isn't a lot of funding for evolutionary science on the molecular level right now, so such a discovery would more likely come about from a virology lab working on reverse transcription (HIV of course being a great example of a virus that uses such a process).

FWIW there are arguments that can be made for not really viewing Buddhism as a religion but more a philosophical school. Of course much of what Jesus is credited with seems similar to a lot of what a lot of modern Buddhists strive for

Certainly any lasting religion offers significant functionality as a philosophy of life--how else are the ethical atheists getting along?

If the argument here is that atheism in many regards is a religion, I generally agree with you. Many atheists I encounter are very entrenched in their selection of non-belief, which is why I describe myself instead as an agnostic. I have seen others suggest that a deity is required for morality, and to this I say hogwash. One only need look in the mirror and consider how un-enjoyable it is to be abused and realize that maybe things might work out better if one were to not abuse others. Of course if pearly gates and fiery pits make the choice easier, than so be it.

But philosophy serves the mind, and religion serves some sort of "soul". Buddhism, to cite one challenge I have with it, holds the notion of re-incarnation, which would seem to require some sort of server-side application to manage that karma database. Sure, God, but, if God, why was I discarding Christ in favor of this Buddhism, exactly?

I'm not entirely sure where you are going with that question. It seems that it could be asked between any two religions easily enough, and only an adherent of any religion X could tell you why their answer is better than the one from religion Y.

From my vantage point I would expect that most people alive at that time would have been uncertain as to which way to go. To an outsider (Jewish or not) the whole Christianity bit likely would have appeared to be a cult, which the ten commandments were warning against. And in the current era at least once a decade or so some guy will make national news proclaiming himself to be Jesus - how do we know that none of these guys are right?

Where I am more or less operating on this point is that the Almighty's overarching requirement is Liberty.

I am still not entirely clear on this statement of yours. How do you see Jesus providing more liberty than the Hebrew god without a savior? Or how about more liberty than the Mormon philosophy? Or the Tao on its own? Of course we could list any arbitrary number of faiths here (you've shared your bit on Islam before so I skipped it this time intentionally) and the conclusion seems to be very personal.

You can't be free to choose God without being free to choose !God, all the way to full-on Nazi genocide.

The Nazis had faith in the Christian god, quite nearly without exception. You can claim it to be a distortion of the Christian faith in a way similar to how Al-Qaeda distorts the Muslim faith, but it is faith in a god nonetheless. It ultimately was not that enormously different from the Christian faith that brought about the crusades.

the fascinating angle is the organizational behavior one. The Pharisees/Sadducees were on top. The early Church was fomenting a revolution.

I'm not convinced that the church had revolution in mind. To me it was more evolutionary, they saw it as a new way to go about things. And of course in evolution new solutions present themselves but they do not necessarily come about with the intent of developing something new or replacing something old, just a way to explore possibilities in a scenario.

Much like a spiritual version of the contemporary Tea Party.

I would argue that the Tea Party already is a spiritual movement, as much of what they pursue they do so out of faith rather than out of fact. However the critical difference is that the church - to the best of my knowledge - did not have a large corporate backing. The Tea Party, on the other hand, gets much of their momentum from their corporate donors - who of course have ultimately the most to gain from the potential success of such a movement.

Jesus of Nazareth was touching on aspects of Judaism that run throughout the Old Testament. He was just thrashing the external, bloody-minded materialism of the Pharisees (see John 3) and calling for internal renewal.

There is an argument to be made that the Old Testament features a god who has no qualms about taking vengeance against man - burning villages, ordering people to kill, turning people into inanimate objects, and of course flooding the entire planet - when so provoked. I don't recall any such things happening in the New Testament. Did the people suddenly get their ducks in a line after that point? To me it seems more like the editors of the Old and the New were so very different in their aims to spread their messages that we found ourselves with two very different books that were bound together.

Now that is not inherently bad, but it seems that this Jesus fellow is all about love while his father had different ideas. Maybe fatherhood brought about a new side of him? Of course I'm still not sure why he didn't stop his son's execution, being all powerful and all...

Re:Comment the first (2)

smitty_one_each (243267) | about a year ago | (#43242369)

The tough part about graduate studies - in regards to accessibility for working people - is of course the general requirement of dropping your regular life to work in a lab for little-to-no pay at very long hours for uncertain time. It is rather unfortunate that we don't have a better solution in place for this; I have met PhD students from European countries for example who are essentially employed at biotech companies while doing their PhD research - one would think we could come up with a similar solution here in the states.
. . .
If you have a vague interest in it in the future I'd recommend watching out for a conference to come to (or near) your town (the ISMB is especially good, though there are others as well), you can get a taste of who is in the field, what they are doing, and what opportunities might still exist with your existing skills.
. . .
Depending on one's degree choice those dreams are often now scattered out past the first (or even second) post-doctoral position. Many people are finishing their PhD and now finding they need a post-doc position in academia first before industry will talk to them. This situation is of course made more miserable by the lack of funding (and hence lack of hiring) in the academic labs.

In my perfect world, I'd write an online game, build it up to a fat property, sell it, and go be a professional student. What's perhaps more attainable is to raise my son to have a lot of intellectual tools, and see if he's turned on by Biochemistry.

The analogy is not all that bad, really. After all in life as we currently know it (if, of course, you exclude rna-only viruses and prions [which can reasonably be called not truly alive]) RNA is the transition media and DNA is the long-term storage. Furthermore as best I recall we had digital memory for computers before we had digital storage
That said, showing that RNA->DNA transition spontaneously in an experiment requires either an RNA-dependent DNA-polymerase (RdDp in virology terms) or an error-prone RNA-dependent RNA-polymerase (RdRp), either of which would need to take place in the presence of free DNA nucleotides or with something that would bring about oxidation of RNA nucleotides. The problem is there isn't a lot of funding for evolutionary science on the molecular level right now, so such a discovery would more likely come about from a virology lab working on reverse transcription (HIV of course being a great example of a virus that uses such a process).

What's intriguing is that DNA itself is a sophisticated database. I sort of inferred that much of the 'junk' DNA is really indexing/metadata, so that 'queries' go really fast. The initial RNA->DNA step would likely be just a dumb "here document", if you will. The RNA needs to keep some state, and is going to build to our modern chromosomes only slowly.
This is why, while I don't doubt the veracity of Genesis, I don't get too literal about the timeframes involved. I also don't put a ton of stock in any of the existing evolutionary theories. When discussing with the Almighty just How It Was Done, my guess is that the human estimates are going to come in kinda low.
Arguments about the origin of life are like Eschatology--they put me to sleep. Let's work toward that repeatable experiment, say I.

If the argument here is that atheism in many regards is a religion, I generally agree with you. Many atheists I encounter are very entrenched in their selection of non-belief, which is why I describe myself instead as an agnostic. I have seen others suggest that a deity is required for morality, and to this I say hogwash. One only need look in the mirror and consider how un-enjoyable it is to be abused and realize that maybe things might work out better if one were to not abuse others. Of course if pearly gates and fiery pits make the choice easier, than so be it.

It's certainly true that ethics and morality are defined in a circular way, but I reject that. I think ethics are "whatever works in court", and morality is whatever is driving you internally. In either case, rationalization remains highly possible. Your theory gets goofy around Stockholm Syndrome [wikipedia.org] . Thus, what's needed to grow people up from barbarism into humanity is some kind of normative feedback. By that I mean the concept of the Holy Spirit in Christianity.

From my vantage point I would expect that most people alive at that time would have been uncertain as to which way to go. To an outsider (Jewish or not) the whole Christianity bit likely would have appeared to be a cult, which the ten commandments were warning against. And in the current era at least once a decade or so some guy will make national news proclaiming himself to be Jesus - how do we know that none of these guys are right?

Where I am more or less operating on this point is that the Almighty's overarching requirement is Liberty.

I am still not entirely clear on this statement of yours. How do you see Jesus providing more liberty than the Hebrew god without a savior? Or how about more liberty than the Mormon philosophy? Or the Tao on its own? Of course we could list any arbitrary number of faiths here (you've shared your bit on Islam before so I skipped it this time intentionally) and the conclusion seems to be very personal.

The point of Christ is that you have your own direct line to God. You stand liberated from all ritualistic requirements to impress anybody under the sun. Nevertheless, if you're truly grasped by the magnitude of Christ's substitutional atonement, then your salvation should drive you toward a maturity that speaks for itself. Not that you won't shank it, often--you will. But, over time, that should diminish. The notion of subjection to drugs, materialism, hedonism, fame, what have you: these should all start to look a little tawdry, and grow boring. That's what I mean by liberty.
Jesus's contemporaries understood that the Law was intended to bring such liberty, but the Pharisees had turned the Law into a racket. Go figure.
Other philosophies and faiths (to include some flavors of Christianity) seem to be either (a) negating the individual to achieve Nirvana, or (b) reducing life to some materialistic video game. I yawn at all that.

The Nazis had faith in the Christian god, quite nearly without exception. You can claim it to be a distortion of the Christian faith in a way similar to how Al-Qaeda distorts the Muslim faith, but it is faith in a god nonetheless. It ultimately was not that enormously different from the Christian faith that brought about the crusades.

I'm not familiar enough with expressions of faith in Nazi Germany to opine. And the Nazi/Islamist tie-in is an interesting one: consider that, after the Qur'an, Mein Kampf is the #2 best-seller in the Middle East. Also that Kampf translates into Jihad in Arabic. So, there may have been some kind of monotheism happening with Nazism, but I wouldn't think it had much to do with the Messiah. Hitler was an eclectic madman for sure, noting that the swastika itself sure freaked me out when I saw it on temples in Korea.

the fascinating angle is the organizational behavior one. The Pharisees/Sadducees were on top. The early Church was fomenting a revolution.

I'm not convinced that the church had revolution in mind. To me it was more evolutionary, they saw it as a new way to go about things. And of course in evolution new solutions present themselves but they do not necessarily come about with the intent of developing something new or replacing something old, just a way to explore possibilities in a scenario.

Having been studying the Acts of the Apostles recently, while the church was not revolting against Rome, it was indeed an insurrection against the Jewish status quo. Which is why Saul persecuted the church, and was himself a punching bag when he morphed into Paul.

Much like a spiritual version of the contemporary Tea Party.

I would argue that the Tea Party already is a spiritual movement, as much of what they pursue they do so out of faith rather than out of fact. However the critical difference is that the church - to the best of my knowledge - did not have a large corporate backing. The Tea Party, on the other hand, gets much of their momentum from their corporate donors - who of course have ultimately the most to gain from the potential success of such a movement.

I wouldn't disagree that guys like the Koch brothers feeding into outfits like Americans for Prosperity and Freedom Works aren't a substantial component. In particular, the leadership and management functions for doing the event setup.
However, you're selling quite a vast swath of sincere Americans who weren't paid astroturfers, but did show up to events, way short here. I've sort of been at ground zero and blogged a lot of this activity, and I'd contend that the Tea Parties are an overwhelmingly clean expression of popular will.

Jesus of Nazareth was touching on aspects of Judaism that run throughout the Old Testament. He was just thrashing the external, bloody-minded materialism of the Pharisees (see John 3) and calling for internal renewal.

There is an argument to be made that the Old Testament features a god who has no qualms about taking vengeance against man - burning villages, ordering people to kill, turning people into inanimate objects, and of course flooding the entire planet - when so provoked. I don't recall any such things happening in the New Testament. Did the people suddenly get their ducks in a line after that point? To me it seems more like the editors of the Old and the New were so very different in their aims to spread their messages that we found ourselves with two very different books that were bound together. Now that is not inherently bad, but it seems that this Jesus fellow is all about love while his father had different ideas. Maybe fatherhood brought about a new side of him? Of course I'm still not sure why he didn't stop his son's execution, being all powerful and all...

Having read the Bible through a few times in KJV and NIV translations, I hear a continuous voice throughout. The whole work speaks of a Creator producing a setting where people are free to choose for/against Him. The OT focuses on externals, i.e. the Law, and refines the Jews as they gain/lose understanding. Don't forget that, after Micah, there is a ~400 gap in 'inspired' writings before Christ (the Roman Catholics will disagree). In the fulness of time, the philosophical soil of the Greeks, the mystical input of the Jews, and the relative political stability of Rome combine to produce a Messiah. The interaction of God and man shifts from the external Law to the internal work of the Holy Spirit. But what's interesting, if you really study it, is that Jesus really isn't anything new; merely the restatement of what the Law meant to get at, but just wasn't delivering.
An elaborate joke? Perhaps. All I can figure is that there will be plenty of time to appreciate it in eternity.

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