text:
"What series of events made you reexamine your faith, and how did you decide that your religion was wanting?"
Because the asker is a good friend of mine, I honestly didn't mind answering, but I asked for a few days to write it all down. I didn't want to just tell the bones of the story and miss any details that I thought were important to me, as part of my own journey into applying rationalism to religion.
Then, not an hour after my first friend asked me, a second, and then a third. I told them basically the same thing I told my first friend, and that they could expect me to answer them in the space of a week or so, because I felt it was an important thing to tell it like it happened.
This is the end result I've come to. There are arguments that you all know and have heard at least ten times. It's long and gets a bit emotional in some parts (which I find a little awkward, so I hope you can forgive me), but this is how it happened.
This is the very brief story of my deconversion. I do plan on making this essay public on my Facebook and my personal blog, but I'd like it to be read by more reasonable people first. I've posted it here just as it would appear on any public site for my religious friends to read (which is why it addresses them and any other religious people). I've had it proofread by my lovely husband, but I'd like it (if any of you endeavor to read this) if you'd let me know if you find any spelling errors. And, as always, comments are most welcome. :)
Let me start this off by saying that I'm not trying to be offensive. I'm not trying to make anyone upset, nor is my objective to 'deconvert' anyone from any faith. I know that by being outspoken about this subject, I am opening myself up to lose family, friends, acquaintances, job opportunities, and even to receive threats.
My main goal is to explain why someone who, just a few short months ago called herself a Christian is longer identifying as such. Not because I need to justify myself (I know why I made my decisions), nor do I feel like I answer to anyone but myself. But some friends have expressed confusion and a desire to understand where my change of heart and mind came from. I'm afraid that I won't be able to touch on every point that helped change my mind, because I do want to make this as brief as possible, while still being true to the way that my loss of faith happened.
This is for you, friends.
Last year, I decided that it was time to re-read the Bible, from cover to cover. It had been a long time (nearly ten years) since I had done that, and I felt that so much time had passed that I should do it again. I had done a lot of growing and changing over that near decade and I wanted to refresh my memory and my commitment to the faith I had. (I'm one of those people that reads all of a software license and the fine print of every advert. It's ridiculous to ignore the actual rules of what you're agreeing to.)
So I did. I read the book and a bit extra (Apocrypha, anyone?) and took notes. There were a few passages that I didn't remember from the last time I read the Bible, and there were some that I did remember, vividly. There were some bits that I didn't understand (I marked those to return to later) and there were some that I understood for the first time, due to recent education through classes and general reading.
There was something else I noticed for the first time while I read. Contradictions. Like, a lot of them. I considered keeping track of them, but I didn't honestly think there would be that many. There were, and it was distracting. I put it out of my mind though, because anyone who knows a little bit about the Bible, knows that it was written by a lot of different people at different times, edited again and again and then translated into so many different languages- it would be ridiculous to think that there wouldn't be discrepancies, right?
Well, no, not if you believe that the Bible was written by the hand of God.
A Few Examples of Contradictions – Are We Punished for the Sins of Others?
[Table from the Skeptic's Annotated Bible]
(After reading these all in the Bible, I didn't agree with the concept any more than I had originally, but I did think that back in the times when the Bible was written, it was assumed your family would be punished for things you did as a deterrent. I found myself making that rationalization- they used any 'law' as a deterrent/motivator for the people during that time period- more and more often.)
'Okay', I figured, 'well, "written by the hand of God" is obviously just a turn of phrase. In fact, I didn't (and still don't) know of any Christian who actually thinks that God sat down one day and wrote the Bible, because the books of the Bible are often called the name of the person who the text is attributed, even if that's not entirely accurate. God didn't literally write the Bible, he inspired many people and those people were imperfect, so the result, divinely inspired though it may be, is imperfect. That doesn't mean that it's not true.'
I moved on, and read further. God punished people for believing lies when they didn't know better (Genesis 12:17, Genesis 20:18), killed people for telling the truth (Numbers 14:35-36), hardens the hearts of people for the purpose of killing them later (because of their hardened hearts- Exodus 14:4-28) and punished children and generations of a family for something an ancestor did (Original Sin- which I had never bought into- wasn't the only instance of this, and that bothered me a lot. See the above chart for other examples).
'But!' I said to myself, 'This God was the God of the Old Testament, the God that most modern Christians don't really take into consideration.' And I thought that was true. The God that demanded and rejoiced in burnt offerings (Exodus 20:24), animal sacrifice (Genesis 15:9-10), slavery (Leviticus 27:3-7), genocide (Exodus 17:11-13), infanticide (Hosea 13:16), rape (Numbers 31:17-18 which also allows for pedophilia and sexual slavery), murder (Numbers 16:49), racism (Numbers 25:6-9), and all other manner of terrible things isn't the God of modern Christians, right? So I put it out of my mind until I got to the New Testament.
I had always been taught that the laws of the Old Testament didn't count in the New, because of Jesus. Jesus's blood was the new covenant. There wasn't any need for the old laws, right?
Except that's not what the New Testament says. In fact, Jesus himself says otherwise. (All emphasis is mine, but no changes have been made).
."Do not think that I have come to abolish the Law or the Prophets; I have not come to abolish them but to fulfill them. For truly I tell you, until heaven and earth disappear, not the smallest letter, not the least stroke of a pen, will by any means disappear from the Law until everything is accomplished. Therefore anyone who sets aside one of the least of these commands and teaches others accordingly will be called least in the kingdom of heaven, but whoever practices and teaches these commands will be called great in the kingdom of heaven. " (Matthew 5:17-19 NIV)
Jesus goes on in Mark (7:9-13 NIV) to criticize people who were not upholding the law by killing disobedient children:
"And he continued, "You have a fine way of setting aside the commands of God in order to observe your own traditions! For Moses said, 'Honor your father and mother,' and, 'Anyone who curses their father or mother is to be put to death.' But you say that if anyone declares that what might have been used to help their father or mother is Corban (that is, devoted to God)— then you no longer let them do anything for their father or mother. Thus you nullify the word of God by your tradition that you have handed down. And you do many things like that."
"Jesus answered them, "Is it not written in your Law, 'I have said you are "gods"'? If he called them 'gods,' to whom the word of God came—and Scripture cannot be set aside— what about the one whom the Father set apart as his very own and sent into the world? Why then do you accuse me of blasphemy because I said, 'I am God's Son'? Do not believe me unless I do the works of my Father." (John 10:34-37 NIV)
Well, alright. So the rules that any moderate Christian doesn't follow, should be followed. Even before my initial re-reading of the Bible, I was aware that most Christians today are cherry-picking which rules to follow and which rules to ignore. We don't kill people for working on the Sabbath or force rape victims to marry their attackers, or any of the 603 commandments (aside from the 10 that everyone knows so well). I've read back and forth between Christians and Jews, the Christians saying that since the Jews were the object and audience of the Old Testament, that the Christians are released from having to follow those rules. Well, even if that is so (which I think sounds more like a cop-out than anything else), why wouldn't Christians want to follow the explicit word of God? Why wouldn't they want to try to be more like God's chosen people, without giving up anything of their own religion? It's in the Old Testament, which is part of the Christian Bible. So, beside the fact that we don't normally like to go about killing people who wear cotton/poly blends, why wouldn't Christians want to try to follow the word of God as closely as possible?
The argument bothered me, the passages bothered me, and the dawning realization of the scope of how much most people don't know about the faith they claim to have was much bigger than I realized. If I asked anyone, I'm sure they wouldn't think Jesus wanted them to kill unruly children. Or, I'd be told that it was a parable or a metaphor. But, in the context, that doesn't make sense. And beyond that, there are only so many things that can be taken as metaphorical, before there isn't another option but to take it literally. "Kill these people for not following rules" doesn't lend itself to being terribly metaphorical when people were actually being killed for not following these rules.
'But', I comforted myself, 'that didn't make Jesus any less miraculous, or God any less real, that just means that the times changed and that we are no longer in need of certain rules'. The idea bothered me, but I put it aside. I told myself that one doesn't have to follow all of those rules to be a follower of Jesus, or to believe that he was the son of God, especially since most Christians flat out ignore most of the rules that they're supposed to be following- even the people who were teaching the rules.
Jesus did do miraculous things in the Bible. He turned water to wine, healed the sick, walked on water, raised the dead, and fed a huge crowd of people with a very small amount of bread and fish. He did things that were called miraculous.. But, if I'm going to do what Jesus asks in the above passage from John 10, I have to believe him only if he does the works of his father. The works of God. I have to hold him to that standard. (Because there were other people in his time frame that claimed they were the Messiah- a brief list of which can be found here and it was claimed that they did miracles as well, so I can see why Jesus would want to be held to a higher standard.)
(I think this is where the 'skeptic' switch got turned to the 'on' position. I've always enjoyed being a relatively rational person, but for some reason it never occurred to me to apply this way of thinking to religion. I suppose it's looked down upon. But as soon as it happened, I couldn't undo what I saw in my rational mind.)
I believed that God made THE ENTIRE UNIVERSE. From atoms to quasars to black holes to earthworms. Viruses, bacteria, howling monkeys and anaerobic microbes. The things we didn't understand then, and the things we're still trying to work out now. The makeup of carbon and the blueprints of stars were his doing. And I'm supposed to believe that Jesus is his son, is actually HIM? The guy who did what amounted to parlor tricks compared to God? The one who left no evidence of any of his miracles? And, in a time where other self-appointed Messiahs were also performing 'miracles'? Heck, even in the Old Testament, when Moses went to Pharoh, the High Priests of the Egyptians were able to perform little tricks too.
Even looking at Jesus's healing of the sick and lame, which I would think was the most miraculous, simply because disease wasn't understood then, his miracles were overshadowed by the fact that, if he had this power to heal the sick, well.. why didn't he heal all the sick? Why let many suffer? Why not do away with all disease? Wouldn't that have converted lots more followers? Wasn't he there to save souls in the first place? Why not do everything in his power (which should have been quite a lot, considering) to help people understand who he was? And, stepping back for just a moment, if Jesus was the son of God, and also God himself, why did he create sickness in the first place? Why allow humans, his most precious creation, suffer? Even if people were supposed to suffer for bad choices (or other peoples' bad choices, depending on if you believe God punishes people for the mistakes of others), I can't help but wonder if babies with malaria really had it coming to them.
I was uncomfortable with how disbelieving my train of thought was (as I'm sure most Christians are that are reading). I didn't like doubting Jesus, the Shepard. Jesus, the lover of the meek and mild. The perfect Prince of Peace.
"Do not suppose that I have come to bring peace to the earth. I did not come to bring peace, but a sword. For I have come to turn
"'a man against his father,
a daughter against her mother,
a daughter-in-law against her mother-in-law—
a man's enemies will be the members of his own household.'"
(Matthew 10:34-36 NIV)
"But those enemies of mine who did not want me to be king over them—bring them here and kill them in front of me.'"
(Luke 19:27 NIV)
Jesus is demanding death to those who didn't want to follow him, for whatever reason. Maybe they just didn't understand him? Maybe they weren't there for his preaching, or to witness his miracles? Maybe if Jesus had healed everyone, they would have known to follow him? Surely they would have known?
"When he was alone, the Twelve and the others around him asked him about the parables. He told them, "The secret of the kingdom of God has been given to you. But to those on the outside everything is said in parables so that,
"'they may be ever seeing but never perceiving,
and ever hearing but never understanding;
otherwise they might turn and be forgiven!'"
(Mark 4:10-12 NIV)
Did Jesus just say that he speaks in parables to confuse others, so that they won't be able to get forgiveness? That's not the Jesus (Prince of Peace?) of moderate Christianity- or at least, I didn't think so.
In fact, there are quite a few examples of how Jesus says he's not intending to be peaceful. There are also examples where Jesus says just the opposite.
Is Jesus Peaceful?
[Table taken from the Skeptic's Annotated Bible]
So that's a little disturbing. A lot disturbing, actually. 'But it's okay!' my apologetic mind screamed, 'Because the Gospels were written at least a generation after Jesus was gone! So chances are that he didn't actually say that!'
Okay. But then what did he say? And for that matter, how can we know he said anything? We know of people who were around at his time, because they wrote things and their contemporaries wrote about them. That's not the case with Jesus. In fact, most of the evidence that pointed to a historical Jesus (with the exception of the Bible itself) has been shown to be either not from his time, or manufactured. So while there may have been a Jewish teacher named Jesus, who was possibly crucified by the Romans, there simply isn't any evidence of him, beside the Bible. (In the interest of space, please see Evidence for the Historical Existence of Jesus Christ here.)
And the portions of the Bible with Jesus in them were written 70-90 years after Jesus died.
I looked up some Christian websites and found that most Christians weren't bothered by any of this. On one Catholic website, there was a Q&A section, and one question addressed this directly. The question was this:
"Why were the Gospel accounts written long after Jesus' death?"
The answer, given by a Father Bob, was this:
"It all depends on what you mean by a long time! The consensus of modern scholarship is that the Gospels were finalized in the form we now know them within several generations of the death and Resurrection of Our Lord: Mark shortly before AD 70, Matthew and Luke between 70 and 90, and John by the end of the first Christian century . Historically speaking that is not a long period of time. It also must be remembered that the Gospels developed in a mostly oral culture, so the stories were told and retold for years before they were committed to writing. Additionally, it is very possibly that the sacred authors drew upon early written accounts of Jesus' ministry and sayings.
The first Christians saw no need to write things down for posterity because they believed that Jesus would be returning in glory very shortly. It was only when it became apparent that the Second Coming wasn't necessarily too expected in the near future that they finally realized the importance of writing down the message concerning Jesus that they were preaching."
The page can be found here
Now, besides the fact that Father Bob gives no sources on his information, what bothered me even more was the fact that he says that 70 to 90 years isn't a long time. Speaking geologically, historically, or even generally, he's right. But when considering the lifespan of the average human during these times is now generally said to be about from 26 to 30 years, 70 years is a lot longer than we consider it to be now.
If there was contemporary written evidence used by the writers of the Gospels, why don't we have that now? What did they take from? To be honest, the closest written documents that the contemporaries might have taken from certainly weren't Jewish (see the table below). And since Jesus was so infamous in Jerusalem, don't you think that some Roman somewhere would have written about the upstart Jewish teacher who was given over by his own people to be killed?
There are other parts of the Jesus story that would have been written about, too. Like why the men of the Jewish council would set aside their sacred traditions in order to meet on the first night of Passover. Or the slaughter of the innocents. Or those dragons Jesus did away with (okay that one is in the Apocrypha, but it's still a Jesus story). Or that Pontius Pilate released a known killer of Romans into the city. Some Roman must have written about that, surely. But we don't have any of that.
And yes, many parts of the story was from an oral tradition, but anyone who has ever told a story, a joke or just recalled an account to someone who wasn't there knows that we all change small details- sometimes not even realizing we are doing it. And these stories were being retold, by many people, as the truth. As, quite literally, gospel. Something to base one's entire life off of. Something to die for.
'Alright!' I said to myself, 'But even if there isn't any evidence of Jesus beyond the Bible, nor of his miracles, that doesn't mean that he didn't exist, and that he wasn't special. He claimed to be the son of God! Not just anyone could get away with that. And he was backed up by many different prophecies from the Old Testament!'
[Table found on Google Images]
Okay. Maybe not that unique. Jesus did have a lot of the same characteristics of lots of the gods and heroes of older oral and written traditions. And maybe those prophecies that were fulfilled, being available to the Jews of the time, were more self-fulfilling than we like to admit. And, being that they were the ones doing the writing, it's not absurd to consider the possibility of some details being changed to fit circumstances.
Considering the likelihood that the Bible had been tampered with, the stories that had been written down were from even older oral traditions, and that even if everything in the Bible had happened, there was absolutely no proof, I had a bit of a crisis.
Since I was having trouble expressing my doubts further than 'there seems to be something wrong here, but I can't quite put my finger on it', I jumped on my computer. In the Google searchbar, I typed in "reasons to believe in God". I figured that if I found some comforting Christian website that helped me understand why none of these things added up in the Bible, that I'd regain my equilibrium, and be able to face my faith without doubts. I found a few very interesting things. Here are a handful of them (and my responses) to show how well looking for a reason to believe worked out for me..
The Earth/universe/eye/brain/human body is designed perfectly.
It does seem that way, at first, but if you examine the claim that the Earth (or universe or eye or brain or human body) is perfect, you begin to see the problems with the statement.
Earth: Earth is about in the middle of the habitable orbit (coined the 'Goldilocks Zone' because it is neither too hot nor too cold). But that habitable orbit is anywhere between about 0.95 to 1.37 AU (or 88 million to 127 million miles) from the Sun, so Mars is in that habitable orbit as well. And, just roughly estimating that there are are between 200 and 400 billion stars, there are bound to be some planets orbiting these stars, some of which are going to be randomly in the 'Goldilocks Zone'. If two out of our eight planets in our solar system have managed to end up in a habitable zone, that's a huge degree of chance that there are other planets that could support Earth-like life.
The Universe: There is nothing about the universe that suggests it was created specifically for us. While we don't understand a lot about the universe, that doesn't mean that we won't be able to understand it ever.
The Eye: This is a particular favorite of a few people who think that the human body is perfectly designed, because the eye acts like a camera, it can recognize an amazing amount of colors, and because it is hard to imagine evolution giving us such an amazing tool. Except it's really not that hard once you think about it, and once you understand basic evolution. It happened in a few stages, the first being a light-sensitive patch of cells(so as to tell when it is light and when it is dark). The second being the patch of cells arranged in a cup shape (so one could tell from what direction the light is coming). The third is the development of a pinhole-like camera, the fourth is the development of a crude lens, and the fifth is the refining of the lens.
The creatures that had slightly more cupped cells in the second phase were more likely to be able to sense movement of predators, and therefore passed on their genes more often. Their offspring (over lots of generations) were slowly beginning to focus on general shapes, and had a great advantage over the offspring who just had the cup-shaped cells. That's how evolution works. (Here's a great video showing the evolution of the eye.)
Not to mention, of course, that anyone who's taken grade school science knows that the images our eyes send to our brains are backwards and upside down. Our brain has to unscramble the images before we can make sense of them. Not to mention humans have blind spots. That doesn't seem to perfect to me, it seems like what arose out of necessity, and it worked well enough to keep it around.
The Human Body: I have heard a lot of arguments that the human body is perfect. Now don't misunderstand, I am in no way saying that it's not an amazing thing. But it's far from perfect. Our wiring is faulty at best (some nerves have to double over themselves to get where they're going), our cells have the nasty habit of liking to suddenly reproduce explosively, and we are constantly at war with mirco-organisms that we are unable to detect using just our senses. Really, just because our bodies have a good map of arteries and veins doesn't mean that our bodies couldn't be put together a lot better.
God gives us moral direction. You can't be moral without God!
Well that's a little disheartening. The idea that the vast majority of mankind is holding off murdering/raping/stealing/blowing up other people and material objects is because they're afraid of some kind of supernatural punishment? I can try to be a good person without needing to be threatened. Actually, it seems more dishonest to only be good because of the looming threat of punishment or promise of reward. Why not just try to be a good person?
If you don't believe in God and that life has a design, you don't think there's any reason to life. God and religion give life purpose!
I don't need to think I'm so important that I deserve a supernatural reason to exist. I'm not special, I'm just another mammal. I don't need a pre-deigned purpose. If I just live my life as a good person and try to make the world a little bit better, I will have done my fellow humans right, and will be very happy with that.
I think it's self-centered and narcissistic to think that in this entire universe, out of all the millions of billions of things going on right this second, that someone would assume that the grand creator of everything would have a specific purpose for me- the barest flash of an inconsequential dust speck.
Hitler/Stalin/Pol Pot was an atheist!
Even if all three of these people were atheists (which isn't true) that doesn't mean that all atheists are homicidal maniacs. That's like saying because the Spanish Inquisition was run by Catholics, that all Catholics are out to torture and kill. I hope that's not true, anyway. On top of that, this 'reason' to believe in God really isn't a reason at all, it's a finger-pointing blame. There are lots of 'reasons' to believe in God that are like this one.
Would anyone die for a lie?
This argument is basically saying that the apostles (and is sometimes extended to all Christian martyrs) wouldn't have died for the sake of their faith if they had not witnessed the happenings firsthand. There are a few problems with this argument, but the simplest and most damning, I think, is that other religions have martyrs too. Does that make those religions absolute truth as well? The followers did believe it enough to die, after all.
Most people have some sort of faith in the supernatural. Even [insert any well-known name here] believes in God!
Just because the majority believes in something does not make it real, or the best option. Two hundred years ago, the white majority thought it was alright to own blacks as property. Just because the majority believed in it did not make it right or the real best option for everyone involved.
Also, even if [insert scientist, celebrity, author, sports star, politician, musician, comedian] does believe in God, so what? That doesn't prove that God exists, that just proves that that individual believes in something that isn't provable..
Something can't come from nothing! So even if everything else scientists say is true, that doesn't account for the beginning of life, so therefore God must exist.
Even though science does not at this point have a good working theory of how life came to be on Earth, there is evidence that abiogenesis is possible (see the Miller-Urey Experiment, it's really interesting). There are theories about the possibility of panspermia as well.
Neither of these hypotheses have to invoke the unexplainable or the supernatural because the universe and our world operate on very specific principles. Furthermore, to assume just because we don't know something now and therefore it must be God's doing and unknowable, is absurd. A long time ago, we thought lightning and earthquakes and hurricanes were signs that God/gods/nature/the spirits/someone else was upset with us. Now we know the causes of these things- and it's not because we've offended Poseidon.
This can also be seen as an argument from incredulity- just because someone cannot fathom how something works means that it couldn't have possibly happened naturally- which is, of course, ridiculous. For instance: I'm not that great at mathematics, though I do find the subject interesting. Just because I cannot fathom the formula that tells us the luminosity of a black hole doesn't mean that it doesn't exist. It does exist. And it was created by someone who had more experience and more training in mathematics than I have. I cannot in good conscience pretend that things don't exist just because I personally don't understand them.
Religion gives people hope and makes them feel safe. Why wouldn't you want to be a part of that?
This was a big one for me, in many different ways- but there was one thing that kept bothering me about the assertion that religion gave hope and warm fuzzy feelings. It was this: even if these beliefs make me feel nice, that doesn't make them true. Do I care whether what I believe is true?
Do I care what I believe is true?
Well, yes. I do. And I realized that making the claim that one believes in God is making a claim about how you think the universe and everything in it works. It's a claim on reality, and everything around us.
To make the extraordinary claim that there is a supernatural God that created everything, knows me, knows my heart, cares about what I (and 6 billion others) do and say, and has the power to bend time and space if he so wanted to, and is all knowing, all loving, all powerful, and everything wonderful- I better have some damn extraordinary evidence. And there isn't any.
There's a book comprised of other, shorter books, written at least 1500 years ago (and some much longer before that) that gives the accounts of some desert people and the rules they had that made sure that their social construct didn't fall apart, and the God they ascribed those rules to (because why would anyone follow rules without an enforcer, and what an enforcer that can get you after you're dead!) . There are even older oral traditions in the book made of smaller books, though most of the mostly-nameless authors can't agree on details. Then the book of smaller books was translated many times, re-written, translated more, and changed by many different men at many different times, sometimes on accident and sometimes not.
A bunch of scribbles written by a desert dwelling people from the Bronze Age on, tampered with until today, is not a good piece of evidence. It is especially not a good piece of evidence for a God who wanted me to get the message that he gave to those people. Anyone with half an ounce of common sense knows that the best way to convince someone of anything is to demonstrate what you are trying to prove. Why would a God, who wanted me to know this message of his love for me, let it be conveyed 2000 years later, through a book that didn't resemble the original book that was written mostly way after the things in the book said happened, and was written by people who hadn't even seen the things happen. Why would this God, who was all powerful and all knowing leave it up to that sort of poor evidence, when he could just show me? And, on top of all of that, give me a rational mind, with which to pull this all apart and come to the conclusion that it just didn't add up?
What kind of God would do that?
If God created the world in all its splendor, why didn't he tell us about it? Why isn't there any science in the book made of smaller books? Why didn't God tell us about bacteria, about small little cells that can get inside of people and make them sick or die? Why aren't there any mentions of other people, all over the Earth? Other languages? Why just this one small place, with this one small mindset, for this one small people? Why isn't there anything in this book but wars and killings and rules on who you should kill and how and when. Interspersed are some truly lovely bits, like "don't kill". No one else sees the irony.
And, even if God was all loving and all good and all powerful, why does he let so many suffer? Why do I see Facebook statuses day after day thanking God for a good parking spot at Wal-Mart, or thanking God that they didn't have to pay as much as they thought they would have to to get their car fixed, or thanking God that they got that payraise they'd been after for six months- when there are children dying of disease and starving in slums and getting raped or sold into prostitution. Why on Earth would a good God allow those great injustices to happen? Even people, flawed as we are, can see that these things are bad.
Their faith is being tested? That's sick. That's cruel and terrible. They're earning a better afterlife? What a disgusting and vile answer. So that the Christians can earn points from a silent observer in the sky by sending crosses and Bibles, or taking the Mother Teresa route and using dirty, work-blunted needles on the sick and dying? Giving no more than asprin to people dying of AIDS, cancer, and malaria? Why won't God hear the prayers of the people who are crying out in pain?
I have tried to remain clinical and reasonable with my answers to these (and other) reasons to believe in God. But the only time I got a good answer to the question, "Why does God grant the prayers of people in the US, who aren't dying in the street, but neglects other people who have life-threatening disease and circumstances all around them?" was when I was answered my own question with this: "Because there isn't an invisible being in the sky who cares about us. Nature isn't sympathetic, and humans are susceptible to catching diseases, being injured and dying. It's a matter of chance, and when one is born in a country with less than adequate water purity, food, and medical supplies, the chance of getting a serious sickness at a younger age goes up quite a bit. Because the world works just like you'd expect it to if there wasn't a God."
At this point, my God was dwindling. The savior I thought I had known was a stranger. The good laws that I had always tried to follow (don't lie, don't steal etc) were eclipsed by laws that I could not in good conscience follow (kill homosexuals, kill those who work on the Sabbath, kill disobedient children, hate and abandon your family etc). The rules that I thought didn't matter because they were in the Old Testament, that actually were upheld in the New. The universe and the world acted in the way one would expect the world and the universe to act if there were just natural laws (gravity, physics) governing, with no help from any deity.
I was upset. I desperately clung to the religion that I wanted to believe in, but with these rules and laws, I couldn't bring myself to commit to it anymore. I needed answers, I needed to know about what much smarter and more educated Christians thought, and how the Methodist church in specific responded to these issues.
I decided to talk to a pastor, and try to get in touch with a few other people who I knew, that knew more about what I was reading than I did. I figured I had talked myself into a corner, that I wasn't able to see the answer because I was too close to the problem. I thought that if I talked it through with someone who was more educated than I was, that it would be more clear to me.
Well, that didn't happen. I did go to a pastor, and I did ask my questions (some of them), and I found a few things that bothered me. When I asked about the Methodist church's stance on some of the rules in the Bible (because I was at that point, still a Methodist), I wasn't given an answer. I was told the pastor's opinion. I was told other Methodist opinions. I wasn't given what I asked for. So I asked more questions. And when I wasn't getting simple "I don't know" answers, I was given more personal opinions and feelings. The few times I was given a Bible verse as an answer, I could usually pull one or two Bible verses that contradicted it. It was frustrating.
Nothing solid, nothing that helped me see where I had been wrong in my train of thought, or in my questions. All throughout the conversation, though, the pastor commended me for digging into the Bible and really trying to learn. He said that my questions were good ones, and that I was a good person (and a good Christian!) for asking questions and using the brain that God gave me to try to know Him better.
We spoke for quite a while, and somehow got to the topic of heaven. He asked if I believed in heaven and I told him that I wasn't sure. I explained that from what I understood of the body and the brain in specific, that the personality and the 'mind' were products of the brain, and that once the brain dies, the memories, thoughts, and personality go with the brain. The control center is dead, and so would be the messages sent by the control center. And I couldn't see anything that made the concept of a soul seem realistic, or even possible.
The pastor's body language and tone of voice immediately changed. He told me I relied on science too much, that I relied on logic and rationalization too heavily. He said I couldn't make sense of an emotional experience. It had to come from the heart. Reason had no place in a church, and that I had to come to terms with that myself. I had to have faith.
In my mind, all I could think was 'But that doesn't make sense! You can't base a huge commitment like religion on just a feeling! You've got to have a reason to believe what you believe, and just saying that you believe it doesn't answer the question, it begs the question!'. In my mind, I had a brief moment of sensation, a surreal feeling of going over some metaphorical bridge. I couldn't put a name to what I had just gone through, so I thanked the pastor for his time, and left.
I realized, driving home from that meeting, that the sensation I had felt was a mental demand to figure out why I believed in God. Why did I think that I knew God, and that God loved me? I made a list. It looked something like this:
I was healed when I was a small child.
I was raised in a Christian home.
Most of the rules of modern Christianity are good ones, although personally I feel that many are outdated and barbaric.
Having a God that watches over me, cares for me and loves me is a good feeling.
A few days later, I went back to that list and just about laughed out loud. It was so self-centered and basically said nothing about who God was or why I believed in him. Here are the replies that I gave to my own list:
I was healed when I was a small child- It seems that doctors and medical staff along with medical technology don't get enough credit these days. Combined with the malady itself, I wasn't on death's doorstep or anything like that, so there is no reason to believe that my general health is attributed to anything other than those doctors and medicine.
I was raised in a Christian home- and if I had been raised in a Hindu home, I'd probably be asking the same questions about those Gods. Nope, not a good reason to base my life on something.
Most of the rules of modern Christianity are good ones- while this isn't false, there is a lot of room for improvement. Not to mention that most evolutionists have shown that ethics evolve within social species, so "don't kill" isn't even that good of a rule. We would know that killing would put us on the outside of the herd, so to speak, even if we didn't have the cognizance to write it down, or to speak it out loud.
Having a God that watches over me, cares about me, and loves me is a good feeling- Just because I want these things to be true doesn't make them true. And just because I felt it in my heart and thought that I 'knew' God doesn't make God real. I recalled a line from Neitzsche, "A casual stroll through the lunatic asylum shows that faith proves nothing."
Just because I want it to be true does not make it true, and just because it made me feel special and good does not make it real (nor does it make me special or good).
I sat back, after replying to my own list and thought. I cared about whether or not what I believed was true. I cared about reality. I cared about proof and evidence and reason. I wanted to follow where the trail took me, and it had led me to realize that there was no proof nor evidence for a God, or any sort of supernatural deity. Not to say that there was proof against the idea. And then I wondered where that left me, the person.
I tried on the label 'agnostic', which seemed at first accurate, but after a while, I began to wonder about the implications. Pure agnosticism, as I understood it, was saying that there was no way to truly know, and therefore God had as much a chance of existing as not. That simply wasn't how I felt. It seemed that the more I really observed the world, the less likely it was that God was a part of it, or even there at all. Why, then, would there be starving children in one war-torn, disease-riddled and Christian country, while other secular countries were doing just fine, even booming?
Atheist then, I thought. There are a lot of negative connotations with the word, and I didn't want to have to defend myself against what surely would cause an uproar by labeling myself as such, but it fit the bill. I didn't believe in any gods anymore, nor the soul, other supernatural events such as miracles, or anything of the like. Not because I wanted to disbelieve, but because there was no evidence to back the claims up. If the evidence showed that these things were real, then I would change my mind. I felt like that was the most rational and reasonable way to go about it.
That night, I was in bed, and the thought occurred to me that eventually, I was going to die. It was a literal 'dark night' for me. I was anxious, I was scared. What would death be like? Would it hurt? Would I be alone? This wasn't the first time I had thought about these things, but the point of view was quite changed. What would nothingness feel like? I didn't want to not exist anymore! I liked existing! I liked being me, having a mind and an opinion and a voice to speak it! I didn't want to disappear into nothingness, I didn't want to simply vanish into the past, as a memory. I didn't want to die.
The next day, tired and a little frazzled, I collected myself and made an effort to look at things through a rational eye. I read a lot of atheist and godless literature that talked about death and dying. I didn't want to hear some reassuring talk about deities and an afterlife. I wanted something that addressed the struggle I had gone through. I wanted to know that somewhere else, someone who had thought the same things I had thought and worried about the same things I had worried about had come through. Not only come through, but been comforted while still facing reality. I wasn't looking for anything to believe in. I don't think I can just believe in something anymore. But I wanted to know that it was possible to come out of the realization like the one I had, and to not be negative or bitter. I didn't want that. I wanted something that addressed the human condition without making it either into a fairy tale or a bleak story with an even bleaker ending.
Some of these essays and papers I found were for people who really were in the process of dying, the sick, injured or elderly. Some were very aloof, and questioned why someone should be afraid of death. I don't think I'm afraid of death, but as someone that's been alive as long as I can remember, I don't really look forward to the day when my metabolic processes stop and I am no longer a living thing. I was a little offended by a few, that suggested that we shouldn't care about death at all. Death does happen to us all, and it is an eventuality, but that doesn't mean that we shouldn't care about it, or at least, not to me. But I'm the sort who likes to face things head-on.
One woman, Greta Christina, wrote about how death in a lovely, very comforting way. She said,
"I don't know what happens when we die. I don't know if we come back in a different body, or if we get to hover over time and space and view it in all its glory and splendor, or if our souls dissolve into the world-soul the way our bodies dissolve into the ground, or if, as seems very likely, we simply disappear. I have no idea. And I don't know that it matters. What matters is that we get to be alive. We get to be conscious. We get to be connected with each other, and with the world, and we get to be aware of that connection and to spend a few years mucking about in its possibilities. We get to have a slice of time and space that's ours. As it happened, we got the slice that has Beatles records and Thai restaurants and AIDS and the Internet. People who came before us got the slice that had horse-drawn carriages and whist and dysentery, or the one that had stone huts and Viking invasions and pigs in the yard. And the people who come
after us will get the slice that has, I don't know, flying cars and soybean pies and identity chips in their brains. But our slice is no less important because it comes when it does, and it's no less important because we'll leave it someday. The fact that time will continue after we die does not negate the time that we were alive. We are alive now, and nothing can erase that. "
In fact, that piece of writing touched me so deeply that I made sure to write down that I wanted it read at my funeral. (The whole article and website can be found here. Some of the articles are NSFW, but I don't see why that article wouldn't be okay.)
And then I couldn't force myself to worry about death. I found myself wanting to be more engaged with my friends, wanting to do more within my community, wanting to help more people more often. Instead of praying for someone, I wanted to actively do something for them. I didn't want to mumble something to a god who might be there, but probably isn't. I wanted to do good for the sake of doing good. And that's what I've based my life off of now. Being the best person I can be, and treating others (other people, other animals, the planet I'm on) well. I don't think we should look for rewards for doing something right. The reward is the right that is done, and I get to share that with others by doing right by them.
So here's the ending of my little tirade. I hope it's made sense in the sensical parts and was distressed in the distressing parts. It was terrifying, taking that first step away from what I was raised to believe, what most of my friends and family believe, and I'm going to have to defend my stance probably for the rest of my life. I'm alright with that.
If you're a religious person and you're reading this, I hope I've explained well why I'm not among your ranks anymore. I hope I have made you think just a little bit, about your own faith and why you believe what you do. Know that my perception of you as a person has not changed, and that I still want to maintain our relationship, whatever it may be. I don't want to cut all ties with my religious friends, and I hope that you don't want to cut all ties with me. I hope we can continue to keep our communication open about this and other topics. Feel free to email me, message me, Facebook me, or even call or text me if you want to discuss this or any other topic. Thanks for reading.
Views: 275
Wow! Very eloquently written, very enjoyable to read.
I wouldn't call it a tirade though, it might be emotional to you but the piece itself is not confounded by it, quite the contrary; your emotions give the necessary human element to better understand your "path" to atheism.
Well done!
I had the same experience as Alejandro. I was compelled to read every bit and plan to save and share it as well. You detail your journey and support your thought process so very well. Kudos!
Gosh, everybody, I'm glad you like it. :) Please, feel free to share it, print it off, whatever. I'm glad my words resonated with you.
Alejandro, I'll make the correction. Thanks very much!


text:
"I consider it completely unimportant who in the party will vote, or how; but what is extraordinarily important is this—who will count the votes, and how." ~ Joseph Stalin
Lament for a Flask of Gin
Column by Jim Davies.
Exclusive to STR
My condolences. I stopped flying as soon as they started restricting liquids in carry-on baggage. Ill be damned if I'll sit in a hot stuffy plane waiting for a stewardess to condescend to pass out a tiny cup of water. Also, the latest "security" procedures would, I think, cause me to lose my temper completely, which would subject me to charges that could lead to years in prison.
Your bottle of gin is symbolic of liberty in America: gone without a trace at the hands of sanctimonious assholes.
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My solution is I don't fly anymore, so I guess anything off the U.S. continent is severely restricted, or prohibited, but given my age I don't believe I shall miss much. Alynski, in "Rules for Radicals" has a possible solution to most political problems, it's exactly what [p]resident [o]bama is using in conjunction with directions from George Sorous. Some how I believe Sorous really wants to be a part of bring the U.S. down since he has collapsed three other countries.
Sorry about the gin, guess you should have had a sticky note somewhere lol.
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subset: commoncrawl


text:
Gender-bending Poison is a gaming favorite. And it's no easy task to pull off her hot pants, whether you are male, female, or somewhere in between.
And do folks ever like dressing up in Poison's skimpy threads. So let's find out who wore the character best?
Regarding the character's gender, the story goes that Poison and her cohort Roxy were originally females, but then changed to transsexuals over concerns how hitting women would go over in the US (a decision that, no doubt, doesn't go down well with some in the transgender community).
As Street Fighter producer Yoshinori Ono explained, "Let's set the record straight: in North America, Poison is officially a post-op transsexual. But in Japan, she simply tucks her business away to look female." The Street Fighter wikia more info, if you are interested!


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text:
Liberace's Ex-Lover Scott Thorson -- TAKES SHOTS TO THE FACE [PHOTOS]
Liberace's Ex TAKES SHOTS TO THE FACE
Liberace's ex-lover Scott Thorson is a man with priorities ... his first stop after getting sprung from jail -- a doctor's office where he was pumped full of Botox.
The photos were snapped in Vegas ... just days after Thorson was released from the pokey where he'd been rotting since February 22.
Thorson -- portrayed by Matt Damon in the new HBO movie "Behind the Candelabra" -- pled guilty to burglary and identity theft in May. He was eligible to bail out while he awaited sentencing in July, but couldn't make bail until last month, with the help of Bunny Ranch brothel owner Dennis Hof.
Once free ... he made a beeline for the Botox doc. We're told the procedure cost $1,200 ... and famed Bunny Ranch prostitute Air Force Amy (above) footed the bill.
Pretty insane ... considering Thorson sued Liberace for cajoling him into getting so much plastic surgery so Thorson would look like Lee ... he got addicted to painkillers and other drugs. So getting more work done seems a bit strange.
Then again, there's nothing wrong with a little prick here and there.
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text:
Wednesday, March 30, 2011
Reporting missing atom types...
(Though the hybridization field is empty, I noticed just now.)
Monday, March 28, 2011
Google Summer of Code 2011: some cool ideas
- tip #1: debian java packaging for taverna jalview jmol bioclipse and cdk? http://goo.gl/12iU9
- tip #2: pathway information, OWL, what can you wish for more? CHEMINF perhaps? http://goo.gl/qInJB
- tip #3: Nescent has the jmol protein evolution again. Great idea, cool graphics http://goo.gl/c0r0j
- tip #4: how much I love the SWT-based Cytoscape in Bioclipse, cytoscape in HTML5 rocks http://goo.gl/jbgWY
- tip #5: #java BioJava3 AA psysico-chemical prop calculations... sounds like http://pharmbio.org to me http://goo.gl/EG7tG
- tip #6: comptox in Orange with AZOrange http://goo.gl/XS0vf with perhaps room for CDK and Cinfony
CDK 1.2.8: the changes, the authors, and the reviewers
The changes
The changes include another few new atom types and fixes of recognition of earlier defined atom types, further widening the scope of chemistry recognized by the 1.2 series. It also has a few other minor fixes, as listed below.
- fixed pdb_atomtypes.xml errors mentioned in https://sourceforge.net/mailarchive/message.php?msg_id=27206678, including the nigly vdwRadius for GLN.CD 3ab7c25
- whitespace-only: alignment of TYR-section 5b51e15
- Added two new authors f72be81
- Fixed a concurrency error, caused by the use of a static field which was not supposed to be static, as the classes are instantiated just to allow customization 9f54afc
- Fixed the use of the proper Convertor 3ea9180
- Added the Co(3+) atom type (fixes #3093644) c368c3d
- Added the unit test phosphine for bug #3190151 851c1a6
- Added a unit test for a phosphor without explicit or implicit hydrogens b35f3bf
- Updated OrderQueryBond in SMARTS & isomorphism matching so that we correctly match when faced with aromatic bonds (rather than just looking at the bond order) 15f64ff
The authors
4 Egon Willighagen 2 Jules Kerssemakers 1 Julio Peironcely 1 Rajarshi Guha
The reviewers
5 Rajarshi Guha 3 Egon Willighagen
Thursday, March 24, 2011
Supplementary files, publishing, and standards #2
Now, it is important to realize there are standards at many levels. Open specifications allow people to implement the specification without having to pay fees, run into patents, etc. To me, an Open Specification is something you can take, modify, and propose to the community as new Standard.
Standards themselves are basically something orthogonal (IMHO, not uncriticized): if something is a standard is just the result of the community picking up and using the specification. Something doesn't have to be Open to be a standard, nor does it have to undergone year-long debates (like HTML5). A standard doesn't even have to be fixed to a version (they can be backwards compatible). There are therefore many kinds of standards, including de facto standards.
These distinctions are crucial. Another is that standards rarely cover everything. For example, it is ridicule to talk about Excel as a de facto standard in data exchange in science. Now, the Microsoft formats are 'Open Standards' (they sneaked in, when the world was complaining). But, they are standards at the wrong level for scientific computation: they define a standard container, and not any semantics. That's up to the user: "Hey, why should I waste a column on units... everyone knows we put in temperatures as Kelvin, ummm, Fahrenheit, ummm... Kelcius, or what is it again the eurotrash uses?"
This problem holds for very many fields, and you see it in many different formulation. Or the whole discussion about ScHTML and PDF, on what is more semantic. Or this one: "Oh, let's use a database so that our statisticians can do there work." Been there, done that.
Now, just to end a bit more positively, here's a group of bright, visionary people using the standards at the right levels in this spreadsheet:
Supplementary files, publishing, and standards
- Journal of Cheminformatics: I hope the Instructions to the Authors improve,
- BioMed Central is going to support Open Data, and
- Nature Chemistry improves publishing chemistry: a detailed analysis.
This week BioMed Central's Iain asked the community how to put their Open Data initiative into practice. There are some good points in the write up, such as:
- Editors and publishers are acutely aware of the limited pool of peer reviewers who are increasingly called upon to help try and ensure the integrity of the published record. The online availability of research data as a supplementary (additional) files has prompted debate about the role of peer review in this non-written material, and indeed the role of journals in publishing this material.
I tried to reply in the blog, but my comment was marked as SPAM because it had more than 1000 characters (update: this seems to have been manually fixed now, thanx!). So much for constructive comments :) So, here goes:
- Dear Iain,
thank you for this interesting and important post! I absolutely agree that some standards need to be set. Scientists have been unable to do this, and publishers can distinguish themselves from competition in doing this right.
Without going into detail what 'right' is (I have very strong opinions on that :), what is important for BioMedCentral right now, is put the advantages so closely in front of the scientist, they can no longer ignore it, or say 'whatever' (which they do now).
BMC must therefore demonstrate what this reuse, reproducibility, etc, practically means. So, Goal 0 must be: do something with the 'additional files': process them yourself and 1) associate every single additional file with facts about that file; 2) index them, and create a search engine to search additional files based on their content, *cross* all BMC journals; 3) provide alternative download formats, showing what it means to use Open Standards.
Open Data is not the goal; it's the means to do science better.
About 1. Every additional file should have a separate web page (or page section), listing not just size, but also the exact format (MS-Excel 2000, rather than 'Excel'... versioning matters!), metadata present in that file (author, creation data, does it have Macro's defined, etc), and statistics about that file (number of sheets in the spreadsheet, number of filled cells, etc).
About 2. It is of utmost importance that we can discover this supplementary information, and it must be easy to search for stuff using free text (e.g. I want to find all additional files across all BMC journals that have 'tryptamine' somewhere in the additional file, even if that information is stored in Excel files *inside* zip files. Current technology makes that very easy, such as Strigi.
About 3. As reuse is the key here, the use of Open Standards are important. This could be stressed by showing that files with Open Standards can easily be interconverted, such as spreadsheets into CSV or HTML tables. Just alternative download formats makes the 'Additional files' more useful, and encourages the authors to ensure that they provide data in the right formats.
Wednesday, March 23, 2011
Tutorials around the OpenTox standard
- The first tutorial will be held Wednesday, 30 March, at 15:00 CET, and
aiming at Java developers who want to learn how to build an OpenTox API
compliant Web service (some acquaintance with Restlet, and basic knowledge of the OpenTox REST API, is necessary).
Participation in these online events involves no registration fee. For more
information, as well as to register, visit
Why I like Linux, it's fast! Or, a quick typo fix in the CDK.
$ git checkout -b 266-14x-typo cdk-1.4.x $ grep -ri Contructs src/main | cut -d':' -f1 | \\ uniq | xargs replace Contructs Constructs -- $ git format-patch -1Patch report is here.
Tuesday, March 15, 2011
Open Standards (Or: "the long list of things that we weren't required to do")
Chemometrics with R
This book is recommended to all bioinformaticians too: many former colleagues from my old department are now in fact working in bioinformatics (see also this BioStar answer).
Sunday, March 13, 2011
Unfortunate (CDK) decisions
The reason why I bring this up, is that I am answering a question on the CCL mailing list on how to convert a XYZ file into an adjacency matrix, and my Groovy Cheminformatics did not have a section on graph matrices yet. And I just ran into the issue that the CDK XYZReader only accepts an IChemFile. Then I realized the book doesn't explain yet why that is either.
It basically comes down that chemical files can contain a wide variety of chemistry. MDL molfiles can contain a single Molecule, but also a set of molecules. Chemical documents in general, think Jmol, can also contain trajectories for cyclohexane (see this nice animation by Bob), etc, etc. And because the CDK is a general chemistry development toolkit, it has to support all. So, we have the IChemFile concept which corresponds to a chemical file, containing a sequence of one or more models, which may be if a single molecules (e.g. geometry optimizations), or multiple models (e.g. MDL SD files). Similarly, each model can contain a variety of objects: reactions, set of molecules, and crystals. Well, you get the point.
Now, at some point, it was decided that being able to convert file formats from one into another might in fact be interesting (think OpenBabel). That's where it went wrong (and if you start git blaming it would not surprise me if I am the center of all evil here). Just to keep it simple, it made sense to have all IO classes at least support ChemFile, because whatever the content, it could always be wrapped in an ChemFile.
So, the answer to the question on the CCL mailing list is a bit more involved than I wanted:
import org.openscience.cdk.*; import org.openscience.cdk.config.*; import org.openscience.cdk.interfaces.*; import org.openscience.cdk.io.*; import org.openscience.cdk.graph.matrix.*; import org.openscience.cdk.tools.manipulator.*; import org.openscience.cdk.graph.rebond.*; import java.io.File; reader = new XYZReader( new File("data/ethanoicacid.xyz").newReader() ); allContent = ChemFileManipulator.getAllAtomContainers( reader.read(new ChemFile()) ) ethanoicAcid = allContent.get(0) factory = AtomTypeFactory.getInstance( "org/openscience/cdk/config/data/jmol_atomtypes.txt", ethanoicAcid.getBuilder() ); for (IAtom atom : ethanoicAcid.atoms()) { factory.configure(atom); } RebondTool rebonder = new RebondTool(2.0, 0.5, 0.5); rebonder.rebond(ethanoicAcid); int[][] matrix = AdjacencyMatrix.getMatrix(ethanoicAcid) println "The adjaceny matrix:" for (row=0;row<ethanoicAcid.getAtomCount();row++) { for (col=0;col<ethanoicAcid.getAtomCount();col++) { print matrix[row][col] + " " } println "" }This code gives this output:
The adjaceny matrix: 0 1 1 1 1 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0
Note that the RebondTool didn't pick up the bond order, but that's not needed for the adjacency matrix anyway.
Getting back on the unfortunate design decision: what would things have looked liked if we had typed our IChemObject reading and writing classes, allowing us to differentiate IChemObjectReader<IAtomContaienr> from IChemObjectReader<IChemFile>. It would have greatly reduced the size of simple programs, or something like the wished-for 50k JChemPaint applet. Right now, pulling in a single reader, will automatically pull in all IChemObject classes. Rather, I would just pull in IAtomContainer, which in itself is too large too. But that's for another blog post.
The key thing to remember is: don't be afraid to add some complexity if that allows you to make other things optional.
New CDK contributors
In one go I also updated the AUTHORS list distributed with the source code. The list of individuals who have contributed source code to the project has grown to 64! Here are a few of the new names:
- Jonathan Alvarsson
- Saravanaraj N Ayyampalayam
- Stephan Beisken
- Dmitry Katsubo
- Jules Kerssemakers
- Uli Köhler
- Scooter Morris
- Carl Mäsak
- Peter Odéus
- Julio Peironcely
- Syed Asad Rahman
- Andreas Truszkowski
- Paul Turner
Friday, March 11, 2011
Pharmaceutical Bioinformatics
Tuesday, March 08, 2011
ToxBank: a data warehouse for (computational) toxicology
Data types we will host include many different types, including my favorite metabolomics. Don't ask me what this will practically mean, but some keywords we already know include RDF, OpenTox, and ToxML. With metabolomics, I hope to squeeze in metabolomics.
And that data warehousing for metabolomics is important was only recently shown be the retraction (via RetractionWatch) of this Nature paper (doi:10.1038/nature03356). The reason was that it critically depended on conclusions from another retracted paper (doi:10.1021/jf021166h), from J. Agric. Food Chem. in 2009.
In this paper, they identified ten chemicals from arabidopsis: butanoic acid; trans-cinnamic acid; o-coumaric acid; p-coumaric acid; ferulic acid; p-hydroxybenzamide; methyl p-hydroxybenzoate; 3-indolepropanoic acid; syringic acid; and, vanillic acid. I hope I have the links to Wikipedia correct, as this was based on names only, as the paper does not seem to list InChIs or even SMILESes. The ten chemical were identified with HPLC and NMR. No experimental data seems to be given. What NMR data did they base the identification on? I have seen pretty interesting assignments of chemical identity in GC/MS and LC/MS, so was quite disappointed to not see the gory details here.
But fortunately, I could look at the raw data. Yeah, sure! Dream on.
In fact, it seems the characterizations of the 10 chemicals was challenged, causing the authors to look again at their data. Unfortunately, they could not find experimental data anymore. The authors write in the retraction:
- We have been unable to find experimental data that document the actual isolation of butanoic acid, trans-cinnamic acid, ...
I am not sure we will see the bottom of this, and see if the authors could have prevented this retraction. However, I do believe the paper was flawed in the first place: it did not give experimental detail allowing the referees to judge the metabolite identification. The referees failed, as the apparently did not find this aspect important enough to have this data in the paper. And, the journal failed clearly, by not having a good editorial requirement in place around availability of data. This is not specific to this retracted paper, nor of this journal. It's pretty much the community standard, despite many calling for years for better standards, e.g. via minimal reporting standards.
Well, maybe journal editors will soon wake up, and make availability of experimental data in papers of this kind (and any type, IMHO) a community standard, and strong standard, such strong that referees can reject papers of papers do not provide this minimal information.
Why? It would have saved a lot of people from doing the wrong thing. The original paper was cited 54 times (according to WoS) and the Nature paper 52 times (up one since the RetractionWatch post). We're bound to see a few more retractions as a result of this, I guess.
So, where I failed to get MetWare going within the Netherlands Metabolomics Center, let's hope ToxBank does better. But given the list of ToxBank partners, I have no doubt about that.
Bais, H., Prithiviraj, B., Jha, A., Ausubel, F., & Vivanco, J. (2005). Mediation of pathogen resistance by exudation of antimicrobials from roots Nature, 434 (7030), 217-221 DOI: 10.1038/nature03356
Walker, T., Bais, H., Halligan, K., Stermitz, F., & Vivanco, J. (2003). Metabolic Profiling of Root Exudates of Arabidopsis thaliana, Journal of Agricultural and Food Chemistry, 51 (9), 2548-2554 DOI: 10.1021/jf021166h
Java Performance...
Reading about Java performance now and then is useful. It's keep you aware of the things that matter and that don't. Via Planet Eclipse, I read a couple of posts from the Java Persistence Performance blog. And today I learned that the JIT compiler can in fact remove the threading support in Hashtable when only one thread is used.


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EDMONTON - Alberta prison guards showed no signs of flinching Saturday in the face of a labour board ruling declaring their wildcat strike illegal and the province's deputy premier claiming inmates were trashing at least one jail.
Guy Smith of the Alberta Union of Provincial Employees says the guards at the Edmonton Remand Centre and another facility in Fort Saskatchewan were vowing to continue their strike until safety concerns are addressed.
"We've encouraged them to stand strong as they've done over the last couple of days. And they know there's other sites across the province that are out as well. And on that basis they've decided to stick it out," Smith said late Saturday.
At least seven detention centres saw guards walk off the job in protest of the suspension of an employee at the Edmonton facility who complained about safety issues.
Inmates have been restricted to their jail cells and striking staff have been either replaced by municipal police or RCMP officers who are backing up correctional supervisors.
Deputy Premier Thomas Lukaszuk refused to say whether guards would be charged for refusing to abide by the labour board's ruling to return to work.
"We will not be negotiating with a union that continues to engage in illegal activities," Lukaszuk vowed during a hastily called news conference at the legislature.
"We will be using any and all legal means to bring order back to these facilities."
Several hundred members of various unions gathered outside the labour board's offices in downtown Edmonton on Saturday as the board members deliberated the province's request for an injunction against the strike.
Many chanted, "Shame," when they heard the ruling. Others called for a general strike.
"What happened in there is what we expected to happen. But that doesn't make it any less shameful," Alberta Federation of Labour president Gil McGowan told the crowd.
"These workers did the brave thing, they did the right thing, for demanding a safe workplace and for standing up for their fellow workers who were disciplined for having the audacity to demand a safe workplace."
The province says the labour board ruling applies only to the two facilities and that it is handling the job actions at the other facilities separately.
Smith said the guards who've been ordered to return to work are well aware of the potential legal repercussions they're facing.
"It's really unfortunate in my mind that instead of sitting down with us and sorting this stuff out, the government has decided to go to the courts and the labour board to turn hardworking correctional peace officers into criminals. It's absolutely shameful," Smith said.
The guards' union has said the suspension of the union member on Friday was the last straw for correctional officers who have complained about the design of the new Edmonton Remand Centre.
Just days before the jail opened, the AUPE said it found five pages of design flaws after touring the facility.
At that time, Smith asked the provincial government to delay the transfer of prisoners from the old remand centre until the changes were made.
Lukaszuk said the facility was deemed safe by occupational health and safety workers, which he noted were also members of the AUPE. He said that if the guards have safety concerns, there are legal remedies that exist in their collective agreement.
He said inmates have been trashing the new Edmonton Remand Centre during the disruption.
He cautioned the reports he is getting are second-hand and that officials were trying to get confirmation, but he said inmates were exploiting the change in routine at the facility in order to cause damage.
"It's heartbreaking that a brand new $580 million facility that taxpayers have paid for is being trashed by inmates right now," said Lukaszuk, who also stressed that no one was in any danger inside or outside the province's jails.
Lukaszuk said there were no reports of injuries. He also said that some prisoners at some facilities were not being confined to their cells and had some ability to move around. Inmates were being fed and were receiving their medications, he said.
The United Nurses of Alberta said a number of its members feared for their safety after the evening shift nurses were ordered to remain inside the Edmonton Remand Centre overnight.
Heather Smith said that at 3 a.m., the nurses there were told by a supervisor to stay close to an escape route.
The union said that as of Saturday morning, all of its members had left the remand centre.
Rory Ziv, a criminal defence lawyer in Edmonton, said it was impossible for him or other lawyers to know what conditions were like inside the facilities during the lockdown. As long as it remained in place, he explained, lawyers couldn't contact their clients.
Ziv said colleagues have been texting him to find out if he has any information, noting it was frustrating for lawyers because many of them only get time to speak with their clients on weekends.
"I'm really concerned for the safety and well-being of the inmates who rely heavily on the guards to feed them and allow them to take part in recreational activities," Ziv said.
"There are others who are more vulnerable because of their mental health or their physical health."
"They need medication or protection from other prisoners."
Alberta justice minister Jonathan Denis said in a news release early Saturday morning that there will be an investigation of the walkout, but he said maintaining public safety and security is currently the province's top priority.
Also on HuffPost


text:
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text:
It looks like the dead will be doing a bit more walking next year.
AMC announced Monday it will launch a third scripted series set in the zombie-filled world of "The Walking Dead."
According to Entertainment Weekly, the show will feature two female protagonists and "focus on the first generation to come-of-age in the apocalypse as we know it." The currently untitled spinoff is set to film 10 episodes this summer to premiere on the cable network sometime in 2020.
The series, created by Scott Gimple and Matt Negrete, expands a "Walking Dead" TV universe that includes the original series, which just wrapped up its ninth season, "Fear the Walking Dead," which begins its fifth season in June, and a previously announced trilogy of films featuring Andrew Lincoln's Rick Grimes character. Producers have not yet said if any existing characters will carry over to the new show.
"Showing audiences an unseen pocket of 'The Walking Dead' universe steeped in a new mythology is a very cool way to celebrate a 'Decade of the Dead' on TV and over 15 years of Robert Kirkman's brilliant comic," Gimple said in a statement.
Assuming next year's seasons of "The Walking Dead" and "Fear the Walking Dead" run for 16 episodes, the launch of the new series could give AMC up to 42 weeks of new post-apocalyptic zombie-killing content in 2020.
"This allows us to come to the marketplace with completely uninterrupted 'Walking Dead' universe content from post-Super Bowl Sunday to Thanksgiving," Scott Collins, AMC's president of ad sales, told Variety in an interview.


text:
SAN ANTONIO – Family and friends gathered Saturday morning to celebrate the life of Jessica Redfield Ghawi, a former San Antonio resident and one of 12 victims of the Aurora, Colo., shooting massacre.
Their goal was to do more than just remember 24-year-old Ghawi. They wanted to celebrate her life.
"She was intelligent, driven, funny, beautiful with a very huge heart. She was also clumsy, a royal pain in the butt at times and very sarcastic," Larry Ramirez said.
A dozen friends and relatives did just that today at the Community Bible Church. With stories and remarks they painted a perfect picture of a spirited, sometimes fiery redhead known for the occasional shenanigan.
"Everyone has been talking about what a firecracker Jessi was so I thought I'd share a few stories," Katy Gardner said. "That girl has been getting me into wild situations since day one."
But tears were inevitable.
"We'll miss you Jessi red. Thank you for everything you did for us," friend and colleague JC Carpenter said with tears flowing down his face.
The sadness was palpable as the reality of Ghawi's absence slowly sunk in.
"I'm hurting with you, and her story will continue to be told," her brother, Jordan Ghawi said.
Her mother, Sandy Phillips, has created a foundation in her name that will fund a scholarship for aspiring female journalists like Jessica. She had moved to Colorado to continue pursuing her dream of a career in sports journalism.
DONATE: Official Jessica Redfield Sports Journalism Scholarship Fund
Ghawi was also setting up a charity called "Little Things," that will gather sporting goods for the families who lost everything in the Colorado wild fires. The fund will also support that effort.
An additional fund has been set up for Brent Lowak, a friend of Ghawi's that was with her in the theater. Donations for the "Brent Lowak Survivors Expense Fund" can be sent to P.O. Box 310176, New Braunfels, TX 78131, or can be made in person at any Wells Fargo Branch.


text:
sent for a test -reward hell or heaven
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Joined: 10 June 2005
Location: Canada
Status: Offline
Points: 8
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Posted: 10 June 2005 at 4:29pm
my question is based on something Shams Zman mentioned in a prior post. It was that we are sent here for a test, and those who fail will be rewarded in hell, those who pass will be rewarded in heaven.
My question... i have adult children, grandchildren, if they do good, that in itself makes a better world for all. I would believe myself a complete failure if my children or my grandchildren , only did that which was good because something was in it for them. So my question is .. if i need something before i do what is merciful or kind, or if i refrain from doing something because i am afraid of punishment, rather than because of the consequences upon others, am i not completely untrustworthy ? Many religions have this concept of reward and punishment after this life, and i have always found it difficult to follow, maybe you can clarify. Thanks for allowing me to ask. berni
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Hello Bernie,
There is a prayer that beautifully answers your question:
"O my Lord, if I worship Thee from fear of Hell, burn me in Hell; and if I worship Thee from hope of Paradise, exclude me thence; but, if I worship Thee for Thine own sake, then withhold not from me Thine eternal beauty." Rabi'ah al-Adawiyyah (d. 801)
You see, we don't do or not do things because we fear hell or want heaven, we act, and worship for the sole reason that we love Allah (God) above all else and want to please Him. This is the goal of all Muslims. I hope this answer helps in what you are searching for.
Peace, ummziba.
Sticks and stones may break my bones, but your words...they break my soul ~
Joined: 10 June 2005
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Ummziba........ first thank you for your welcome within the other forum for new persons, and thank you for this message. Although i cannot conceive of torture (hell) being justified under any situation here or in the next life, (my people have outlawed it in canada, and i certainly expect as much from G-d) i can appreciate the lesson within the prayer you forwarded. Again Ummziba, thank you....... have an excellent day eh ......
Shams Zaman
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Joined: 20 March 2005
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Points: 135
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My dear and respected Bernie!
May peace be on you!
Your logic and conviction is wonderful but I fear it is not commonly applicable in this world and most people won�t think the way you think. Why you play rugby or a football match once there is a trophy for the winner?? Why you study hard if there is an academic prize for the position holder?? Why you fight a battle in which you have a victory in the end?? Why you perform an act of bravery once you can fetch a medal at the end?? By virtue of your logic all these actions should be a complete failure for you and rest of the world.
Let me ask you something: If personal conviction is the criterion for wrong and right then why people do wrong things? Surely you will say that because some are unable to differentiate between right and wrong. For some this may be true but most do it even once they know it is wrong. So once we know that it is wrong, why we commit crimes like murder, rape, stealing, torture etc. And if someone refrains from these due to the fear of going to Jail or being punished under the state law, would it be the state failure or success??
Let me answer it as well, because all may not be as positive in their thinking as you are, so if the end result is peace and harmony, whether it be through conviction or threat means justify the end.
We have read the saying of Lady Rabia Basri! But remember she was not an ordinary women, she was one of the greatest of the saints, both among men and women and had completely submitted to the Will of God. Her love for God comes from within and not due to the fear of Hell or love for heaven. Not everyone thinks that.
Islam is not only meant for the intellectuals. An ordinary man may not find it easy to leave the rewards of seen at the cost of unseen or to undergo all these hardships and sacrifice without any tangible reward at the end. For some, this may be a mean deal, but if the end result is achieved it is perfectly acceptable, and the end result in this case is submitting to the Will of God by obeying him.
For the moment let us suppose that there is no reward for our good deeds neither is any punishment for wrong doings, so how many would like to refrain from evil acts like drinking, bribery, stealing, womanizing, murder, rape, torture and snatching own benefits at the cost of others, indeed very few. A lot may not like to sacrifice so many attractive things around just for the simple reason that this is the way it should be and they shouldn�t do it for it is not to be done. The sense of sacrifice will evaporate. To sacrifice for what, at least I would never do that. Yes the one who is wealthy and contented may like to do so but not the deprived one, neither the poor nor the mischievous.
These people will argue that what they would achieve by submitting to God once they are deprived of all the benefits and this is the only life why not to live it in comfort and luxury at whatever cost? Why to sacrifice and why to care for others? They will take care for themselves. In fact these questions were posed to Prophet Muhammad (mpubh) by the rich pagans of Makkah.
Similarly we see that the concept of reward and punishment exist in all the tiers of our worldly life. All states follow the same principle. If this clause is removed the world will soon turn into a chaotic and torturous place. Why the
Who gave us this life? Indeed God, we owe it to Him. He blessed us with so many of His blessings without which there would have no meaning of life. Like our senses (to hear, taste, talk, see, comprehend and express), feelings to share love and affection, mind and brain to think and prosper (we could have been living like animals without it), sweet water to drink, taste food to eat, warm clothes to wear and you can keep counting.
So if some of your son or grandson behaves very rudely after you had given him shelter, food, clothing etc what will you do to him? Or if he says that I don�t recognise you as my grandmother! What will be your feelings? You will be hurt or may even feel like beating him. What would you do to your TV set which doesn�t obey you, once you try to put it off it turns on and once you try to put it on it switches off? You will certainly throw it away or break it.
But God�s actions are not reactionary or hasty. He has given us a mandate of submission to His Will (as every other thing and creature do, like all physical laws obeys God by remaining constant and none can defy God, likewise moon can�t fall on earth and sun can�t run away from this solar system). But we Humans were given the choice to either submit to God�s will or to defy it. And God is not unjust so if someone submits to His orders he will be rewarded and anyone who rejects His commandments will be punished. Both can�t be equal.
Another commonly given logic is, (also mentioned by you): �if they do good, that in itself makes a better world for all. I would believe myself a complete failure if my children or my grandchildren, only did that which was good because something was in it for them.� This may be a fine logic for some but not for all. First who is to decide that what is right and what is wrong? One may give absolute logic in favour of drinking or womanising, some may prove bribery as absolute normal; some may declare homosexuality to be a personal and private affair. While others may destroy half of the mankind in the cause of National Interest, (like of the United States), and some may kill thousands of innocent in the name of Nationalism as was done in case of World War 1. All give conclusive logic and reasons to justify their actions. Presently all seems to be convinced that whatever set of rules or religion they follow is the right path. George Bush directs his actions towards eliminating evil and not for any reward while Osama also holds the same claim. So are all individuals� right in their claims? Even once every individual had a varying sense of judgement?
If everyone is not right then who is right and;
What is right? And;
Who set the rules of what is right and what is wrong???
The answer is simple God created this world and He sets the rules for this world. Obviously he has set one set of rules for us.
If there is no divine reward or punishment then God is unjust (and this is absolutely impossible). Why? Because! This world is imperfect, and God can�t do that to us, by creating an imperfect world and forgetting us.
Imagine of a child who got birth in the poorest country of
He did not opt for this kind of life. He would have also loved to live like of a Saudi King or a Royal family member. But to be born in a family of his choice was not an option for him.
Secondly, how would you deliver justice to special cases like of Adolf Hitler or Genghis Khan or Mussolini etc who killed millions of innocent people?? (You can certainly feel the pain much more than me for being a Jew as it appears to be from your writing). But none of them could ever be brought to justice. Even if they would have, merely by hanging them to death or giving them the lethal injection, by no means can be termed as justice. The only justice for them can be delivered in the Hereafter through the hands of God.
God doesn�t act abruptly or hastily. Like if God�s book (Quran) is being desecrated or some one is being murdered or being raped or being tortured and he or she cries for God to seek for His help, will the wrath be let loose on the criminal? Surely, no angel will descend to save him/ her and neither God will immediately come for his rescue. So does this mean that God is unkind or can�t see the injustice being done? And if He can see why doesn�t He act or react?
Because God is the most wise and he doesn�t take abrupt decisions. Certainly all good and evil acts will be registered and the punishment and reward will be given in the hereafter according to the deeds. If God acts abruptly then no one will commit any such act and there will be no test. He certainly gives us time to repent and seek forgiveness, but once he gets hold of someone then it�s severe, too severe (hell).
Unfortunately we all think that we have got the ticket to heaven or salvation. Christians, Hindus, Jews, Muslims, Buddhists etc all think the same way. But this is not the case; salvation is not in keeping particular types of names, or in belonging to a particular race or believing in absurd ideas. The criteria to qualify for heaven has been spelt out by God in the following words:-
�Swearing by the (age of) time o For surely complete mankind is in loss o Except for those who believe, and have righteous deeds, and exhorts each other to truth, and enjoin each other for patience o�
So the conditions are simple:
So anyone who fails in the above mentioned criteria he has qualified for hell. But we cannot pass a judgement on this because God says that He may forgive all the sins of a person pertaining to Him (not to any other person) except for Associating Partners With Him.
So it�s all up to His discretion either to forgive all the sins or to punish for them all which pertains to Him alone. Anyone who associate partners with Him or deny His existence will never be forgiven like Christians have declared Jesus (pbuh) as the son of god. Some Jews proclaim Ezra (Aziz (pbuh)) as son of god, while other says Jacob (pbuh) wrestled with God and God could not overpower him and is equal in strength. Some Muslims proclaim Muhammad (pbuh) as part of God while others claim the Caliph Ali or various saints and Sufis as intermediates between God and man and some even worship them. Hindus worship idols in the name of God while Buddhism and Jainism are not even sure of the existence of God. And worst of all a large portion of population has opted to become an atheist.
So majority of mankind is off the right path and there has to be one righteous path because all can�t be right with all these contradictory beliefs.
To conclude; if you follow the above mentioned criteria (4 points) no matter whether, out of the fear of Hell, or for the lust for heaven, or for the reason that you simply think this is what you should be doing as a good human, or out of love for God, you are on the right track and you will Insha-Allah (God Willing) be rewarded in the life hereafter.
Following books can provide a good help to understand the true path and the answers to most common questions troubling the people in the West:-
1. Struggling to Surrender by Jeffery Lang.
2. Even Angels Ask by Jeffery Lang.
3. Road to Makkah by Muhammad Asad (ex name Dr. Leopold Weiss, converted from Judaism)
4. Islam at the Crossroads by Muhammad Asad.
5. Islam Versus the West by Maryam Jameelah (ex name Margaret Marcus, converted from Judaism)
6. Western Civilization Condemned by Itself by Maryam Jameelah.
Shams Zaman
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text:
BioOriginality Principle.
BioOriginality states that any original information materials are in fact the product of previous data, information and knowledge.
Therefore, the origin of any kind of mental work can not be claimed and dedicated solely to one person.
* Here, bio means organic network transpassing time and space.
This in practical terms means that there is no "founding father" for knowledge.
The term BioOriginality is tightly associated with BioLicense.
In practice, if any web site, media, or an intellectual project on Earth is under BioLicense (hence under BioOriginality Principle), there is no 'original' founder.
Any present and future person/people is the "perpetual founder" of the project. For example, the original BioPerl project license said that anyone who edited a single character of the BioPerl module becomes the owner and main participant of the BioPerl. Any active person in such a project is effectively the founder (as intellectual properties keep changing and even evolving).
BioLicense is under BioLicense.
Therefore, the founder of BioLicense, and any other projects that uses BioLicense, is YOU who is reading and contributing in anyway and affects the world in an indirect and direct way in the future.
See also
Biooriginality: This is the prime site for biooriginality concept.
Synthetivity.com: Synthetivity is a term to replace creativity. Nothing is created in this universe but only synthesized.
Biopedia.org | FreeScience.net | Biojustice.org | Biosociety.org


text:
Law enforcement agencies from across the U.S. have reached out to Jalopnik for help with car identifications since your input was "critical" to solving a hit-and-run last year, among others.
Today, we bring you an unusual story involving a pair of hit-and-runs in Philadelphia from last week.
What was unusual wasn't the crime itself, but the victims themselves. It's not a regular occurrence to hear about a 10-year-old getting struck by a hit-and-run driver on a Thursday afternoon and then her 14-year-old sister suffering that Saturday night. But, that's exactly what happened to Sarah and Kylee Givens on, respectively, March 7 and 9.
While the driver who struck 10-year-old Sarah has since turned himself in, Philadelphia Police are seeking the public's help to track down the hit-and-run driver who left Kylee with a ruptured spleen and broken ribs.
They released a video on Thursday afternoon hoping they could do just that. A portion of their press release reads:
The Philadelphia Police Department is seeking the public's assistance in identifying the suspect who hit a 14 year-old female in Wissinoming.
On March 9, 2013, at 8:30pm the complainant was at the intersection of Cheltenham and Torresdale Avenue when she was struck by a white vehicle that fled the scene. The vehicle was last seen traveling north on Torresdale Avenue then east on Van Kirk Street. The complainant received serious injuries as a result of this incident.
Vehicle Description: White two door, unknown make, possibly newer model with tinted windows.
Thoughts? Hunches? Let's talk it through and see if we can help them out.