Archive for August, 2008

Part 1: The Cytochrome-c tree, anomalies, and why anomalies exist

(Disclaimer: I’m not in the field of bioinformatics.)

Cytochrome-C is a protein involved in turning food and oxygen into energy. It’s found in Eukaryotes – which means all multicellular life (plants and animals) and some single-celled life (fungus and yeast). The fact that it’s so ubiquitous gives us the opportunity to compare evolution over wide sections of life on earth. After compiling the protein sequences of nearly 100 species, I ran some genetic analysis on it. Here’s how the results look:

The basic pattern of descent is shown pretty clearly with this data. Animals you’d expect to be related are clustered into groups. For example, primates are a subset of mammals, and apes (including humans) are a subset of primates. Humans, Chimpanzees, Gorillas, and Orangutans all have an identical protein sequence of cytochrome-c (and the DNA sequence varies slightly among them). Birds are a branch out of the reptiles group. Whales are clearly part of the mammal group – not the fish group.

It also shows how ridiculous it is when creationists make statements like:

“There is not evidence yet to claim how the Earth was created and no evidence to connect the family of apes with the family of man.” – Utah state Superintendent of Public Instruction Patti Harrington (Source)

However, there are a few anomalies in the series. They are:
– Frog appears inside the “Fish” group. It also doesn’t appear next to bullfrog.
– Horsfield’s Tarsier appears with rat, mouse, and guinea pig. Tarsiers are related to monkeys (it should actually appear roughly where kangaroo does).
– The kangaroo (a marsupial) appears inside the placental-mammal group.
– Honey-bee appears outside the ‘insect’ group and near starfish, earthworm, and snail.
– Bat appears near seal and dog.
– Why don’t mammals appear as a subset of reptiles (since mammalian ancestors were reptiles)?
– Why don’t reptiles/amphibilians appear as a subset of fish (since terrestrial vertebrates evolved from fish)?

First of all, genetic studies of individual genes have certain limitations. While the general pattern of decent can often be shown from a single gene, the details can be confused due to inherent problems of small datasets. Creationists sometimes use genetic studies on a single gene as if it’s perfect truth, and if anything varies from accepted evolutionary theory, they’ll argue that those problems are evidence that evolutionary theory disagrees with the facts. The problem is this: genetic studies on individual genes is a little bit like a public poll. Even if you perfectly randomize the people answering your poll, it’s still susceptible to inaccuracies. For example, if you randomly call phone numbers, you might discover that 9 out of 10 respondents support a particular candidate, even when the reality is that it’s a 50-50 split among the public. Studies of single genes have the same problem, and, in both cases, this is a problem that is more likely to occur with a small dataset.

How do these problems arise with genetic data? It has to do with mathematics of mutation, and limited information.

When genetic data is analyzed, we look at a sequence, compare differences, and create a tree which describes the relationship pattern. So, for example, if we have four species with the following protein sequence:
Species1: DAAAAA
Species2: AAAAEA
Species3: ACAAEA
Species4: ACAAEA

We could construct a few different trees to describe the situation. If we assume “AAAAAA” is the ancestral sequence, then the tree looks like this:

We would then infer that this pattern represents the splitting of species and mutations over time. In this case, Species2, Species3, and Species 4 probably inherited the E mutation while they were all one species. Species3 and Species4 acquired the C mutation while they were one species. However, it’s possible that all of these mutations happened independently, like this:

Statistically, it’s unlikely situation #2 would happen. It requires that Species4 happens to get exactly two mutations, and those two mutations exactly match the mutations in other species. However, it’s not statistically impossible. And since it’s not impossible, it will happen with a frequency equal to its likelihood. It’s also possible that a mixture of the two situations occurs.

So: when two species have the same mutation, it might be that they gained it through common ancestry, or they might simply be coincidence. When dealing with large numbers of mutations, you can quickly sort-out which is which, but with fewer numbers of mutations, the correct interpretation is less certain.

These are some situations which can make the ancestry ambiguous, and lead to erroneous phylogenetic trees:

First, let’s pretend we have a 100 amino-acid sequence. Let’s also say that each location can contain two different possibilities (the other 18 amino acids disrupt the protein’s function, killing the organism).

(1) The more species there are, the more likely two of them will have an identical mutation by coincidence. If we have two species, and each of them have an independent mutation, then the odds that they will be the same mutation is 1 in 100. However, if we expand our example to contain 15 species, each with one independent mutation, the odds that two species’ mutation will match becomes extremely high. In fact, on average, there will be one matching mutation. (The fifteenth species has a 14% chance of ‘hitting’ an existing mutation because there are already fourteen separate mutations in the group.) The situation gets worse and worse the more species that are added to the group. That common mutation might be interpreted as “a common mutation acquired through common ancestry”, but that’s an incorrect conclusion.

(2) The more independent mutations a species has, the more likely it is that one will overlap an existing mutation in another species. Imagine that our two species have each acquired 20 independent mutations. What are the odds that one of the mutations in Species1 will match a mutation in Species2? Statistically, we can expect that around 4 mutations will match ( 0.20 * 0.20 * 100 locations = 4 ). Again, the situation becomes more likely with more mutations. None of those mutations were actually acquired through common descent, but it will be interpreted as commonly acquired mutations.

(3) Back mutations also make the situation ambiguous. Let’s say we begin with four species with this sequence of mutations. Species 4 has a back mutation (changing “E” back to “A”).

The resulting sequences are ambiguous. What should the interpretation be from the sequences alone?

Based on the resulting sequences, it’s not quite clear what the correct interpretation should be – at least not without some outside information (from other genes, etc). And if you construct a tree with the wrong interpretation (2 or 3), creationists might jump on it and say, “The genetics says that Species2 and Species3 are more closely related than Species3 and Species4. But, evolutionists claim Species3 and Species4 are more closely related. Evolution contradicts the facts.”

The problem of back mutations increases as the number of independent mutations increase. This is because the possibility of a back mutation is proportional to the number of total mutations.

Explaining the Anomalies:

In most of the anomalies shown above, the problem involves a single species which has no close relatives on the chart, and has acquired a large number of mutations. This increases the incidence of situations #2 (large numbers of independent mutations coincidentally overlapping existing mutations) and #3 (back mutations erasing actual descent information). And large numbers of species (#1) gives lots of possibilities to find matches. Take the honeybee for example:

There is a small area of commonality (section A), and a large area of independent mutations (section B). Cytochrome-C contains 104 amino-acids, and the honey-bee and snail versions differ at 26 locations. What happened was that a few mutations overlapped, it matched slightly better than other species on the chart (perhaps due to back mutations), so it erroneously placed it next to ‘snail’.

The frog and kangaroo follow this same pattern. While one would expect ‘bullfrog’ to be a close relative of the frog (i.e. Western Clawed Frog), they actually differ at 15 locations. The large number of differences shows that their common ancestor lived a long time ago – which shows just how ancient the ‘frog’ group is. And Kangaroos are the only marsupial on the chart. The Kangaroo protein sequence should be equidistant from all placental mammals, except for some random coincidental mutations. It just happens that those coincidental mutations placed it near the primate group where it clearly doesn’t belong. In fact, different analysis algorithms place the kangaroo in different locations, indicating how tentative its current placement is. Including some other marsupials in the list should stabilize it’s location outside the placental mammal group.

Bats appear near seals and dogs. That seems odd. Although, bats are actually a pretty ancient species as far as mammals go, so there might be some coincidental mutations. (And as for the hippo being close to the same group – well, based on the length of the line, that’s a pretty thin conclusion.)

None of these four species have any close relatives on the chart, they have a large number of independent mutations, so the software probably found the best match based on coincidental mutations.

Horsfield’s Tarsier is also an anomaly. It should appear at the base of the primate group. Either this is just a case of an odd coincidental mutation placing it elsewhere, or perhaps tarsiers shouldn’t be classified as primates. (Some people have suggested that.) In the end, a larger genetic analysis should clear up what’s going on.

The other anomalies involve the placement of mammals inside the reptile group, and terrestrial vertebrates as a subbranch of fish. In fact, mammals evolved from a branch of ancient reptiles that was separate from the ancient animals that gave rise to modern reptiles. From the Tree of Life website (1,2):

And terrestrial mammals descended from lobe-finned fish, which is separate from the ray-finned lineage of the four fish shown (tuna, carp, zebrafish, and pufferfish). From the Tree of Life website (1,2):

(Another interesting thing to notice from the Tree-Of-Life charts is the large number of animal groups that have gone extinct. All the little yellow crosses indicate extinct families of animals. It looks like nearly 90% of all animal groups have gone extinct. I guess those were the projects God started and then scraped.)

Up Next: How Creationists use and abuse Cytochrome-C data

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Well, the DNC is right around the corner. I live in downtown Denver, and I can already see some extra people in the area. (If anything crazy happens, maybe I’ll have pictures or video.) Lots of groups have been coming in to try to influence the Democrats. Lots of protests are planned – and many of the protesters are anti both parties. They think both parties have sold out, and they prefer to support Nader or some other lost cause. Well, the other day I walked outside to find a bunch of political fliers on cars. They’re the work of Randall Terry (anti-abortion activist, Christian extremist):

Randall A. Terry is an American political and conservative religious activist and musician. He founded the pro-life organization Operation Rescue in 1987 and led the group for its first 10 years. He has been arrested more than 40 times for his anti-abortion activities. (Link)

(More on Terry here, here, and here.)

The fliers pretend to advocate a white-supremacist candidate (“Smith”) who supports slavery for blacks. Obviously, you’re shocked and appalled. Then, it does a switch: it says that abortion is murder, and murder is worse than slavery, therefore, you cannot support a candidate who allows abortion any more than you can support a candidate who advocates slavery. The white-supremacist fake-out certainly catches people’s attention. It’s the shock-politics of the pro-life movement. A second flier then talks about Obama’s voting record regarding abortion (he supports it, McCain opposes it).

During the anti-abortion pitch, the flier talks a great deal about how a Christian should vote, but ironically enough, the heavy focus on how a “Christian should vote” resonates as the kind of rhetoric you’d expect from a Southern redneck advocating segregation.

No Christian may in good conscience vote for any candidate, from any party, for any office, who supports the slaughter of children by abortion. Don’t be seduced! If you vote for Rudy or Hillary or any pro-choice candidate, you share the sin of child-killing, and betray the very Law of God.

The flier (click to enlarge be appalled):

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[Via BoingBoing] Rob Cockerham did an experiment on Craigslist; He pretended that he found some money. Here’s his post:

And some of the responses he received:

Jack- My wife and I where shopping at Mervyns and lost 260.00 it was one fifty one ten five twenties and one one hundred dollar bill. We where at the Mervyns on Plano Rd. In Dallas please let me know if you found any part of this money we would greatly appreciate it. (Fri. 4:40pm)

Rob- Hi Jack, I’m sorry, I found the money in the shoe department at the Camp Wisdom Mervyn’s store. Good luck. -Rob (Mon 10:31am)

Bella- Hello I was shopping at the mervyns on camp wisdom with my family I was in the shoe department and jewlrey department. somewhere in either department I lost three hundred dollars. and I am going out of my mind ! please email me back and let me know if you found it. I have been worried sick. thank you (10:35 am!!)

Rob- Hi Bella, That is the same store where I found the money, but I found almost $800 wrapped in paper. I’m sorry. It might even be from the store itself, so I’ve been planning to go and ask the manager if their deposit was missing or something. Good luck. – Rob (Mon 12:50 pm)

Eric- I saw your post on cl just as I was going to put one up. my boss told me about cl. I lost some money at mervyns on camp wisdom I had just come from the bank and stopped in to get some sneakers. the money I lost is my rent money. it was wrapped in paper and was 780.00 . my wife is needless to say unhappy with me for loosing it. I called the store and no one has turnend it in. if you can email me back. thank you. eric (Mon 12:54 pm)

Bella- thank you for emailing me back. someone just called me who found my money! so thankfully I got it back.

Rob- Hi Eric, Ok, thanks for writing. I called the store and tried to talk to the manager to see if it might be misplaced or stolen from the register, but she was not available. I hung up after 7 minutes on hold. Anyway, I’m waiting for them to call me back too. I want to be sure I have the right person because it was a lot of money. Can you tell me anything about the paper? -Rob

Eric- It was wrapped in white paper, I am loosing my mind paniking because that was almost my whole pay how could I possibly recoop that you know|?

Rob- The money I found was wrapped in magazine pages, so I don’t think this is the right money. Good luck. -Rob

And that was it. Each represented personality came from a separate, long-established yahoo mail account.

I can hardly believe it actually happened… that someone actually thought I would fall for their ever-more-specific claims. It felt like the same person coming up to my “Free Candy” booth four times, wearing lame disguises with each visit. And just so you know, the money in Dallas was wrapped in the centerfold pages…from Oprah’s “O” Magazine.

Since they were all from longstanding email addresses, I have to wonder: Was it one person who had a whole series of fake email addresses to pull-off scams? Was it a group of friends/coworkers trying to get the money?

(More craigslist “lost money” experiments here)

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Golf Astrology

I nominate this for the most ridiculous book I’ve seen all year. It has a chapter for each astrological sign, giving you personalized advice on what you should wear on the golf course, the preferred signs of your golf partners, and whether or not you should buy used clubs.

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(Militant Atheists shown below.)

Apparently, in game testing, some people had an issue with the game ‘Spore’ because it includes religion. I think as games mirror the real-world more and more, it’s impossible to avoid taking-sides or editorializing. Even the game ‘Civilization’ included religion. The problem is that you can’t give religion a role without implicitly taking sides on the issue. Some people think religion is like a virus, others see it as false but useful for civilization, and others see their religion as the one true way – humanity’s lifeline to God. You can’t really put all three roles into a game and please everyone. Will Wright comments on the complaints:

Eurogamer: You describe yourself as an atheist; take the so-called militant atheists like Richard Dawkins and Christopher Hitchens, who see faith uniformly as a bad, negative and dangerous thing. Do you see it more benignly, even if you don’t necessarily believe?

Will Wright: Oh, I definitely see it more benignly. I see a lot of benefit and danger in religion like anything[…] I think our bigger fear was that we didn’t want to offend any religious people; but looking at the discussion that unfolded from this thing, what we had was a good sizeable group of players that we might call militant atheists, and the rest of the players seemed very tolerant, including all of the religious players.

Most of the articles ended the quote right there (1, 2, 3, 4) – making atheists and ‘militant atheist’ virtually synonymous. But, he goes on:

And most of the atheists were very tolerant as well. I didn’t expect to hit hot buttons on the atheist side as much; I expected it on the religious side. But so far I’ve had no critical feedback at all from anybody who is religious feeling that we were misrepresenting religion or it was bad to represent religion in the game. It was really the atheists!

My only issue with Will Wright’s comment was his use of ‘militant atheist’. In any other context, the word ‘militant’ means violent, taking up weapons, and killing people. (In fact, the images above are from the first page of google images when you search on “militant”.) It’s silly to use that to describe atheists who are complaining. These guys didn’t show up at his house with AK-47s and technicals. But that doesn’t stop everyone from jumping on the theme: ‘Militant atheists’ up in arms over Spore’s sim-religion.

Now, “hardline atheist” I guess I’d be okay with that in the sense that it’s more accurate (though it has negative connotations), but at least it doesn’t erroneously hint at violence and killing.

Update: It seems that Spore doesn’t just include religion as a method of managing your civilization. In fact, it would seem odd to complain about that, and many other games have done the same thing. Rather, when you reach the Civilization phase of the game, you can choose a military, economic, or spiritual path. Choosing the spiritual path gives your people access to magical powers (Faith Heal, Black Rain, and Messianic Uprising). I guess atheists had a problem with some realism (simulating a planet’s evolution Intelligent Design over billions of years), coupled with unrealism (gaining magical powers based on religion).

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The Satanic Jews thought up an evil plot [the Holocaust] to be rid of the burden of disabled and handicapped, in twisted criminal ways. While they accuse the Nazis or others, so the Jews would seem persecuted, and try to benefit from international sympathy…

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If you read atheist’s blogs, you probably already know about John Freshwater. From wikipedia:

The local school board voted to dismiss Freshwater in June because “Freshwater preached his Christian beliefs about how the world began, discredited evolution and didn’t teach the required science curriculum, the board says. He was told to stop teaching creationism and intelligent design, but he continued to do so, an investigation found.” In addition, the school board released a report showing that Freshwater branded a Christian cross into one student’s arm and several teachers complained for eleven years about Freshwater’s incorrect teaching of evolution. Two of the parents’ of the children branded filed a lawsuit against Freshwater and the school district. He gave an extra-credit assignment for students to see the pro-intelligent design movie Expelled:No Intelligence Allowed, using Jonathan Wells’ discredited Icons of Evolution and work by convicted felon Kent Hovind. According to CNN, “The report also cites evidence that Mr. Freshwater told his students that ‘science is wrong because the Bible states that homosexuality is a sin and so anyone who is gay chooses to be gay and is therefore a sinner’.”


The Ten Commandments together with other posters of a religious nature were posted in Mr. Freshwater’s classroom. Most were removed after Mr. White’s letter of April 14, 2008, but at least one poster remained which Mr. Freshwater was again instructed to remove on April 16, 2008, but did not do so.

Mr. Freshwater engaged in prayer during FCA meetings in violation of the district’s legal obligations for monitoring such organizations.

I’ve heard a few things lately that the right-wing/Christian media have focused specifically on one issue: keeping a Bible on his desk (which is not any kind of offense, and certainly not one that would get him fired). They continually harp on this one issue and ignore everything else – creating the perception that Freshwater was fired for one and only one thing: keeping a Bible on his desk. Obviously, this gets the Christian / conservative / pro-free-speech people riled up because it creates the illusion of a heavy-handed liberal establishment firing a guy for having a Bible on his desk – as if the “liberals” are out to ban religion, and having a Bible can get you fired from a job.

Here’s a video clip from Breitbart.tv titled “Hundreds Turn Out to Back Science Teacher Fired for Keeping Bible on His Desk”. See how long you have to watch the video before they even mention anything Freshwater did wrong (other than the allegation that he kept a Bible on his desk).

And now watch the ensuing hysteria:

We know it is almost criminal to carry a Bible and worse to have it in your desk at a public school–if you are a techer.This is the state of things in our nation,where christian science teachers are no longer welcomed at public schools nation wide,just because they believe in the Bible… We are in the days in which christianism is gonna be outlawed in the US,while paganism and atheism is embraced gladly by the masses that have hardened their hearts and hate and fight any mention of God anywhere in the country,especially in the public arena…May God help us!!!!!!!!!!! (Source)

It seems obvious this man is being persectuted because of his faith. I would go so far as to call it a witchhunt..being accused of burning a cross into a student’s arm as if he is some crazed zealot because it is well known that he is Christian. To fire a man with over his faith would be UNHEARD of…

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DonExodus2 is a YouTube user who does a lot of evolution videos. They’re pretty good stuff, and I heard about his videos via thunderf00t (who created the “Why People Laugh at Creationists” series). Recently, he posted a video about why he’s a Christian. In the evolution battle, I think it’s important to have Christians on the side of evolution because it’s too easy for Christians to dismiss atheists who make arguments for evolution. They can simply say, “Well, evolution is a required part of their non-belief in God, so they’re exaggerating the support that evolution has” – and avoid serious thought on the subject. While his evolution videos are pretty good, his reasoning wasn’t very persuasive when it came to Christianity. Maybe I should just ignore his unpersuasive pro-Christian arguments rather than raise questions about the theistic evolution position. The theistic evolutionists seem to get hit from both sides: the atheists don’t really like their theism, and the creationists (ranging from young earth creationists to old-earth/common-descent IDists) accuse them of undermining evidence for God.

I’m also amazed by the degree to which people can argue the science side decently, but then put forward weak arguments in other subjects (the existence of God). You would sort of think that their thought-process would identify and eliminate their weak ideas when they can’t form a decent argument in favor of them. But, maybe everyone has their pet-ideas that undergo less scrutiny than their other ideas. I was also interested to see how a theistic evolutionist deals with Old Testament stories which they don’t believe actually happened. (My own background was being raised by young-earth creationist parents, so I know their viewpoint: the Bible is literally true back to the six-day creation, and any science that contradicts that view is wrong.)

Belief versus Knowledge – 1:20-2:20
He makes the argument that belief and knowledge are different, but “extremely related things”. I actually agree with him on this point – belief and knowing are both part of one continuum. We might say that our certainty about a particular idea ranges from 0 to 100. 0 means “we know it isn’t true”. 100 means “we know it’s true”. The only thing I that I absolutely know for certain is “I think, therefore, I am”. Everything else – including the reality of the external world – is less than 100. What we call “knowing” might correspond to ideas in the range of 0-5 (know it’s not true) and 95-100 (we know it is true). “Belief” appears in the middle area. The problem is that religious apologists will paint this picture of belief and knowledge being next-door neighbors separated by some hair-thin line, and then ask why two things can be a hair’s breadth apart (say, a 94 and a 95) can be considered to very different things. Effectively, they want to create the illusion of belief and knowledge to be nearly the same thing. That might be true in the case of a 94 and a 95. The problem is that many religious apologists will perform the magic trick of trying to take something that is uncertain (say a 40 or a 70) and create the illusion that it is no different than something that’s a 95 – because belief and knowledge are “nearly the same thing”. It’s a kind of rhetorical magic trick.

Evidence for God – 2:20-3:55
There are many things that cannot be tested empirically, does that mean that it’s wrong? No. And belief in God is exactly one of those things. The nature of God is something which by very definition cannot be tested empirically. So are things like whether or not you love someone, or your personality….

A couple problems with this. First, atheists do not attempt to answer the question of whether God exists simply by using the tools of science. Atheists are not using a null-hypothesis for God, finding no evidence to gather and than deciding there is no God. Second, if we assume an interventionalist God (as described in the Bible), then God would have an effect on the world, and that effect is (by definition) measurable. There are plenty of studies done on the effectiveness of prayer and meditation. They have no effect. Now, you can always say that God didn’t intervene in that particular case, but the statement that “The nature of God is something which by very definition cannot be tested empirically.” is clearly untrue. It might be the case that your particular God cannot be tested empirically, but the “nature of God” certainly does not rule-out the possibility of testing. I can think of plenty of tests (prophecy, miracles, appearing as a pillar or fire – as in the book of Exodus, Jesus could still be walking around the earth preaching 2000 years after his crucifixion, etc) that would validate God’s existence. And, since DonExodus2 is part of the Creation-Evolution debate, I could also add that it’s theoretically possible for there to be ample evidence that the earth is only 6,000 years old. What if nothing carbon-dated to more than 6,000 years? What if there were no fossils of any ancient animals? What if Noah’s Ark was found on Mt.Ararat? And what if we discovered that humans all descended from a single family who lived in 2250 B.C.? What if angels and ghosts were as obvious as the existence of birds in the sky? What if you could talk to loved-ones after their death (and not in that sham-medium way), but as easily as you talked to them when they were alive, and they validated the existence of God, angels, and heaven? There are lots and lots of things that *could* be true about the world, and would work to validate the Bible and God’s existence, but the evidence for the existence of God (both in the present and the past) seems to be as elusive as evidence for aliens, bigfoot, the loch-ness monster, etc. It’s true that a lack of evidence can’t allow you to say that God or bigfoot doesn’t exist, but DonExodus2 is wrong in saying that God is inherently outside the possibility of scientific examination.

Another reason why I personally believe in God is due to personal experiences. Which leads to the discussion about subjective versus objective evidence. For example, hypothetically, if I saw Jesus appear to me last Tuesday and bring me a milkshake, I would be a fool not to take that into account when evaluating whether or not Jesus really exists. On the other hand, it wouldn’t do very much for you, which is why it’s subjective evidence. And subjective evidence is exactly what can make one person’s view of something rational while another person’s perhaps not. And, that’s personally, one of my reasons for believing in God.

Unfortunately, he doesn’t tell us what this subjective evidence is. Further, I would think that people all over the world with a variety of religious beliefs have this subjective evidence as well. Although, their evidence (like Christians) is due to coincidence, confirmation-bias, misunderstanding, etc. I sometimes wonder about theists who win the lottery. My guess is that many, many lottery winners attribute their win to God. I’m unsure how someone would even go about talking them out of the idea that God caused them to win. Afterall, winning the lottery is absurdly unlikely. Of course, even in a godless world, someone would occasionally win the lottery – and those wins would have nothing to do with God. My point is simply this: even if DonExodus2 had subjective evidence as “solid” and unlikely as winning the lottery, it’s not necessarily good evidence – even if he thinks it is.

The second thing would be .. the supernatural. I believe in things like ghosts and that… I believe that 99% of all ghost encounters and things like that – “miracles” – are absolutely garbage. They didn’t happen. But I simply believe that it is much more likely that just one, just one, of the billions of independent encounters of ghosts and things like that since the beginning of recorded history – it’s more likely that just one is accurate than that they’re all wrong… the existence of ghosts and stuff like that would be indicative of a soul … and that would necessitate a supreme being.

I really don’t follow his thinking on the idea that it’s more likely that one ghost story is true versus all being false. If 99% are false, then an additional 1% doesn’t seem like much of a stretch. Is he saying that whenever there are a lot of reports about a particular phenomena, that some of them are bound to be true? For example, there are lots of reports of UFOs, bigfoot, loch ness monster, fairies – does that mean some of those reports true, and we should accept the existence of UFOs, bigfoot, loch ness monster, fairies, or any other popular cultural myths? What about Muslim and Hindu miracles? There are plenty of reports, does that mean some miracles are true? My only guess is that he starts from two premises: ghosts and miracles are possible + there are lots of reports of ghosts and miracles = some reports probably are true. (Which then creates a feedback loop: some reports probably are true, therefore, ghosts and miracles are possible.) My own opinion is that you can’t take the mass of reports as indicative of anything. Nail down one good ‘ghost’ report, and then you can conclude that ghosts exist.

Now on to evolution and why Christianity and evolution are not in conflict… [the numerous authors of the first five books of the Bible, and their different perceptions of God] all testifies to Genesis being best taken allegorically. Another thing, is that something can be allegorically true, without being literally true… Original sin is still a useful allegory because it explains to simple minds and primitive people why we’re [still?] here, an example that will suffice until science can come around because, but keep in mind that primitive minds can’t and could not accept descent with modification and most primitive minds still can’t, the second thing that is does is … it explains our sinful nature … as a result, we need to pay for those [bad] things, and be forgiven, and be saved.

Well, I’m sure the young earth creationists will love the label of “primitive minds”. I would add that it’s Genesis that is holding them down, because people insist on theological teachings over scientific teachings. Ready to hear something crazy? My dad was a science teacher for three decades and a young-earth creationist the whole time. How did he do it? The Bible was the final say on everything – afterall, it was the literal word of God, and that means it automatically supercedes any possible scientific evidence. There is literally no possible evidence that could overturn something written in the Bible – that would be the equivalent of proving God to be a liar. (And, just to make sure he doesn’t experience cognitive dissonance, there are plenty of young-earth creationists groups who are willing to tell him exactly what he wants to hear: that evolution is a total sham.) Does he have a “primitive mind”? I don’t think so. His beliefs are based on a commitment to the Bible – and I think smart people believe in young-earth creationism due to a religious commitment. If Genesis had an evolutionary story rather than a six-day creation story set in 4000 B.C., I don’t think they’d have a problem accepting evolution.

But, regarding DonExodus’ arguments, I see several problems. First, “original sin” doesn’t appear in the Bible until the New Testament. Jews don’t believe in original sin, and it is certainly never talked about in the Old Testament. Are we supposed to believe that early Christians (around the first century AD) had more primitive minds than the early Jews hearing about Judaism for the first time (a millenia earlier?) But, let’s ignore the 1st century Christian idea of “original sin”, and consider the Genesis story. The ancient Greeks played with some ideas involving spontaneous generation of lifeforms centuries before Jesus was born (though, admittedly, centuries after Genesis was written). The ancient Hindus also believed that the universe was *extremely* old. So, this provides another counterexample to the idea that humans needed some super-simplistic young-earth explanation because their minds weren’t capable of understanding it. To take DonExodus’ view, means accepting the idea that God had to talk-down to humans two or three thousand years ago, giving them an oversimplistic explanation of human origins. Even back then, humans were pretty smart, and they could’ve accepted an evolutionary-like explanation. Further, wasn’t the Bible supposed to enlighten the minds of those ancient people? Instead, it codifies a young-earth creationist viewpoint, and now we’re fighting about it several millenia later? Regarding the idea of “sin” as an explanation of the need for forgiveness, I don’t buy that either. You can talk about sin, imperfection, and the need for salvation/forgiveness without talking about Adam and Eve. In fact, Muslims have this kind of system. They don’t believe in original sin, but they do believe in “falling short of the glory of God” (to quote from the New Testament). In fact, “original sin” was never a big concept when I was growing up (in a Christian household). Rather, it was always emphasized that my individual, personal sin generated the need for salvation and forgiveness. (Something reinforced by Jesus when he said, ‘If you even look at a woman with lust in your heart, you have sinned and need forgiveness’.) All of this means one thing: the Genesis story is entirely unnecessary for the purposes of establishing “original sin” (a first century Christian idea), or the need for forgiveness/salvation (doesn’t the fact that no one perfectly follows the 10 commandments establish that?).

It’s also important before we begin this to preface this by saying, “Don’t quote-mine”. And that’s very important because both sides do it, too. For example, Sam Harris at idea-center did an awful, awful, awful, really shoddily -researched talk where the entire [premise] of his discussion and the entire point that his thing was based on was a quote-mine from Luke in which Jesus is saying, where he said that Jesus said, “bring any non-believer before me and slay him at my feet”.

Well, I’m not sure what Sam Harris’ main point was, but DonExodus’s explanation of Luke 19 didn’t really do it justice. In the parable, God is obviously the ruler. The part about “slaying unbelievers” isn’t telling Christians to slay unbelievers. (If Sam Harris’ point was that Christianity tells believers to kill unbelievers, that’s incorrect.) However, it is a description of what will happen to unbelievers when Jesus returns – he will have the unbelievers killed. DonExodus’ explanation makes it sound like Jesus does not approve of the actions of the ruler. In reality, Jesus is the ruler, and he’s talking about his relationship to the believers, and what he will do to the unbelievers at some point in the future. Here’s a quick excerpt of the story (Luke 19):

Luke 19:11-15
While they were listening to this, he went on to tell them a parable, because he was near Jerusalem and the people thought that the kingdom of God was going to appear at once. He said: “A man of noble birth went to a distant country to have himself appointed king and then to return. So he called ten of his servants and gave them ten minas. ‘Put this money to work,’ he said, ‘until I come back.’

“But his subjects hated him and sent a delegation after him to say, ‘We don’t want this man to be our king.’

“He was made king, however, and returned home. Then he sent for the servants to whom he had given the money, in order to find out what they had gained with it.

Luke 19:26-27
“He replied, ‘I tell you that to everyone who has, more will be given, but as for the one who has nothing, even what he has will be taken away. 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.”

It’s pretty clear from the context that Jesus is the ruler who is going to ‘go away’, and then return. That would also make him the ruler who will say, “those enemies of mine who did not want me to be king over them—bring them here and kill them in front of me”.

Another commonly quote-mined verse is Isiah 13:16 where it says “their infants will be dashed to pieces”… and people often attribute that as God saying that, but that’s not the case whatsoever

Regarding the Isaiah 13 verse (“Their infants will be dashed to pieces before their eyes; their houses will be looted and their wives ravished.” Isaiah 13:16), which DonExodus’ claims is quote-mining, it’s true that they are the words of an oracle, but the chapter makes it appear as if the oracle is delivering God’s message, and it’s not clear whether the oracle’s words were or weren’t authorized by God. I think a case could be made either way. I wouldn’t use that verse as being “God’s definitive words according to the Bible”, but I don’t accept the “quote-mine” allegation because that implies deliberate lying. (Link to Isaiah 13) Whether Christians have to accept it as God’s message (versus the oracle’s ignorant ramblings) – that’s debatable, but claiming it’s God’s message does not require lying. I would also add that some Christian apologists have used Isaiah 13 as an example of a fulfilled divine prophecy. So, Isaiah 13 is ‘just an oracle’s ranting’ when Christians want it to be, and it’s a fulfilled divine prophecy which validates the Bible when other Christians want it to be. I don’t think it’s fair to accuse atheists of ‘dishonestly’ claiming Isaiah 13 is God’s message when Christians are also claiming it as God’s message.

Additionally, killing babies is certainly not out of character for the Old Testament God. Afterall, God killed all the firstborn of Egypt, he authorized killing all the men, women and children during the invasion of Canaan, so I don’t know why DonExodus suddenly has a problem with the idea that God would authorize killing the infants of Babylon. Maybe he denies that God authorized any of the Old Testament killings. (And, actually, DonExodus does make this argument later.)

.. Many of those things in tradition they were just passed down as oral stories, they were passed down orally. They weren’t written down, for most of the Old Testament for several millenia, and you have to keep in mind what exactly that does. Over a period of time that long, anyone who has ever played telephone will tell you that the story can change quite a bit during that time. The gospels, on the hand, which aren’t to be take allegorically, were written, or were compiled as early as 10 years after Jesus’ death… [That] answers two things: what is literal, and why are there horrible things in the Bible.

He talks about oral tradition for “several millenia”, but there’s no way it was several millenia. Moses (who did not write the Bible) would’ve lived around 1300-1200 B.C. The Plagues of Egypt (including killing the first-born) would’ve happened around 1300 B.C. The invasion of Canaan (and divine commands to wipe out nine different groups of people there) would’ve happened around 1200 B.C. (although, some divine commands to wipe-out neighboring tribes happened much later). Earlier, he talked about authors of the Bible around 850 B.C. The dead sea-scrolls have large parts of the Old Testament carbon-dated to around 200 B.C. – and it was certainly written-down centuries before that. But, I’ll pretend he said “passed down orally for several centuries” rather than “several millenia”. Second, he doesn’t explain why stories from oral tradition are supposed to be taken allegorically, rather than literally. Is oral tradition simply incapable of transmitting literal stories (of course not). How did oral tradition end up with a simple little six-day creation story? Are we supposed to think that God gave the Jews an evolutionary story, and the oral tradition completely morphed it into an allegorical story about Adam and Eve, and an entire ancestral line of “begats”? Heck, even the New Testament claims to trace Jesus’ lineage back through King David, Abraham, Noah, and all the way back to Adam. I have a hard time believing that the lineage in Luke 3:23-38 is supposed to be literal for a few generations, and become entirely mythological as you get back to Adam.

Regarding the corruption of the Bible due to oral tradition, I think cultures that depended on oral tradition tended to take it a bit more seriously than a game of telephone. I’m also doubtful about how much oral tradition could’ve corrupted the “real story”. I mean, there are mass killings in the Old Testament. It seems unlikely that the real story was “help your neighbors”, and that was accidentally turned into “Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.” (Numbers 31:17) after a few centuries. The other problem is that the Bible is the way human beings would understand God and who he is. If it is corrupted, then God should make an effort to set the record straight. And given that “God” is an all-powerful, omniscient creator of the universe, there are plenty of ways to do that: he could talk to human beings, he could send angels, he could create a book and deliver it to humans. Afterall, this is the same God who (supposedly) talked through a burning bush, created the Ten Commandments, sent angels to proclaim Jesus’ birth, and stopped Paul on the road to Damascus and asked him, “Why are you persecuting me?” In fact, in the next section, DonExodus will say that he doesn’t think God speaks “with this billowing voice from the clouds”. But, Matthew 3:17 claims that’s exactly what God did: “And a voice from heaven said, ‘This is my Son, whom I love; with him I am well pleased.'” So, it’s inconsistent to say that God couldn’t have set the record straight when he apparently does speak to human beings.

The fourth thing is: why are there so many horrible things in the Bible? And again, historical interpretation of the Bible is very important in understanding that. And there are a couple reasons. For one, our view of God has changed in the past 3,000 years. We know more about God now than we did 3,000 years ago, and I don’t think could really argue that. … Well, what’s often said and what’s understood can be two different things. I don’t believe personally that God speaks with this billowing voice from the clouds, and it’s very clear. So, what could be conveyed and what could be understood and acted upon are two different things.

I don’t entirely follow his reasoning here. He seems to be arguing that human’s view of God changed, and, so, the reason there are atrocities in the early part of the Bible is that the Biblical authors misunderstood God and falsely attributed actions (plagues of Egypt) and commands (kill the people of Canaan) to God that God never did or commanded. The problems with this argument are, again, that God should be capable of communicating his desires and actions. DonExodus seems to act as if God is speaking to humans with two tin cans connected by a string. In reality, I expect God to be more capable of communicating his desires than the most accomplished human speaker. And, God can also make sure the writers of the Old Testament get things written down accurately – afterall, if the Bible is “God’s word”, I would expect that He has a very strong interest in making sure things get written down accurately, and that He is portrayed accurately to future generations.

In fact, I remember having this same discussion with a woman who was a Christian. She didn’t like the “wives submit to your husbands” section of the New Testament, and argued that the New Testament authors got it wrong. I made the same argument to her: if this is “God’s word”, then He should have a strong interest in making sure no human corruptions are added – thus foisting bad teachings on the next two thousand years of Christian believers. Of course, my actual point was that the New Testament was not written by God, but reflected some views and culture of the New Testament authors.

This also reveals a problem – why you interpret which sections are corrupted and which are “God’s word”, you can end up cherry-picking to construct a theology that suits your personal views. Don’t like the atrocities of the Old Testament? Easy: they’re corruptions. Don’t like “wives submit to your husbands”? It’s a corruption. Don’t like Biblical teachings about homosexuals? It’s a corruption. If the Bible was the word of God and it contained corruptions, then God could hardly blame people for subjectively deciding which sections of the Bible to ignore. But, once people start ignoring certain sections, there will always be people who will ignore parts they shouldn’t, and pay attention to corruptions that they should ignore. All of this strengthens the impetus for God to make sure the Bible is accurate.

Why Jesus? … I have the attitude that … It’s better to embrace reality, regardless of how cruel, than persist in a delusion, regardless of how tingly and warm it makes us feel. And let me start by saying Christianity does not give me the warm fuzzies whatsoever. So, that’s nothing with my motivation.

Okay. Remember this quote because it will come back to haunt DonExodus in a minute.

Why do I believe in Jesus? One is that the apostles died for what they believed, and they directly knew Jesus. And there are a couple possibilities as to why they would do that. One would be that they were lying, but that’s not really probable simply because most people aren’t willing to die for something that they know is a lie. They could simply be delusional, which I would discount based on a couple things, one being I Corinthians 15, in which Paul [says that five hundred people saw the resurrected Jesus].

First of all, the fate of the twelve apostles is not entirely known. About half of them disappear from the New Testament after the first chapter of Acts. I talk about this while reviewing Strobel’s book (search for “few weeks after the crucifixion” in this post). Maybe they believed Jesus rose from the dead, maybe that’s simply a fiction included in the gospels. They don’t necessarily have to believe in the resurrection of Jesus or in any miracles in order to risk their lives for Christianity. Many, many people come to believe that their cult leader is God. In fact, there’s an interesting interview I had read of a former Waco/David-Koresh follower. He left the compound about a month before the siege. Obviously, he’s no longer a believer, right? Wrong. He seemed racked by the fear that David Koresh was God, and he missed his one opportunity to go to heaven. This is a guy who knew David Koresh, and continued to believe after his death. When you read Jesus’ writings, it has lots of parables about faith, maintaining belief, and the result of ‘falling away’. For example: the parable of the bridegrooms in Matthew 25 is about the importance of the believers maintaining their faith. This could easily cause many of Jesus’ disciples to devote their lives to being ‘good servants’ – even if Jesus never did a single miracle, and never rose from the dead. It’s incorrect to assert that they wouldn’t have risked their lives for Christianity unless Jesus actually rose from the dead. And, on that topic, here’s an transcript of an interview with one of David Koresh’ surviving followers:

Narrator: Although most of the followers of David Koresh are now dead, the story is not over. Some of his disciples survive & remain fanatically devoted. This worries authorities. Rick Kirkham found one woman living in California who is holding on to Koresh.
Karen: We were driving along & we had the radio on when we heard that the ATF decided to go in & start punching holes & whatever.
Narrator: When government agents began their assault on the compound in Waco, Karen Doyle was not there. She & a handful of other followers were returning home to California after celebrating Passover outside the compound.
This house in LaVerne, California, was once the home of David Koresh; in fact, three of his followers still live here. It is the only property left in the Koresh holdings. And ironically, one member who still lives here, Karen Doyle, says she would have rather been at the compound at the time that it burnt to the ground than here. She contends that those who died in the fire along with David were the lucky ones.
Karen: I wish I had been there from the very beginning. My wishes were that I was inside with the rest of my friends & family.
Interviewer: You wish you had been in the compound when it burnt to the ground?
Karen: Yes, I do.
Interviewer: You would have burned to death!
Karen: I suppose I would have, but you know, we don’t look at physically losing this body as a tragedy or….

Interviewer: Your sister perished!
Karen: So to speak, yes.
Interviewer: Are you sad by that?
Karen: No, I’m very happy for her. I mean, I know I will see her again. So….

Interviewer: What about the 17 children?–These young kids who were inside the compound who perished in this horrible fire, how do you feel about them?
Karen: I’m very happy for them. I know that I will see everyone again. It’s not a matter of your own sadness or anything like that, because I have faith & I know that God has everything in control, & I’m just very happy for them.

Regarding Paul’s (I Corinthians 15) claim that 500 people saw the resurrected Jesus, well, I’ve seen this interpreted by Christians as, “Paul wouldn’t make such a bold claim unless he could back it up – there must’ve been 500 people who saw Jesus.” First of all, Paul never says who these 500 people were, so it would’ve been difficult for anyone to verify. Second, I highly doubt any of the Christians would’ve pressed Paul on the issue. Third, was Paul simply repeating a rumor he’d recently heard? Was the rumor later denied by the very people who supposedly saw Jesus? Fourth, it’s not entirely clear what happened when these supposed 500 people saw Jesus. Did a bunch of Christians see a man dressed in white appear mysteriously on a hilltop, and they jumped to the conclusion that it was Jesus? Maybe 500 people were outside, and some of them declared that it “must’ve been Jesus appearing above them on the hilltop”. Others might’ve been unsure about the idea. But, the ones who “know” that they “saw Jesus” told everyone about it. Now, “all 500” had “seen Jesus” (even if some of them were doubtful about the claim). Then, the rumor gets passed around between the different Christian communities and becomes “fact”, and all the questionable details get left out because everyone wants to believe and everyone wants to tell a nice little faith-confirming story. (I actually know of several cases where Christians have exaggerated details because that’s what the audience wants to hear. Heck, Paul could very well be doing the exaggerating in order to buttress the faith of Christians in Corinth.) I have no doubt a bunch of believers could talk themselves into that. And once it’s “established fact”, well, no one would be able to deny it. Because Paul gives us no details, we’re in a very bad position to actually evaluate the situation. I would also add that I don’t believe in other mass-sightings of religious figures. For example, I think the Our Lady of Fatima appearance was a result of mass-hysteria, suggestion, expectation, dehydration, and exaggeration.

But, lastly, I believe in Jesus because if you live your life truly according to the gospels, two things will happen: One, you’ll be a happier person. And, two, the world will be a better place…

Remember that quote I told you to remember back in 7:50-8:35, where he says it’s better to embrace a hard truth than a nice fiction, and then added, “Christianity does not give me the warm fuzzies whatsoever. So, that’s nothing with my motivation”? Well, now DonExodus is saying that Christianity does make him happier, and that happiness is one of his reasons for being a Christian. Anyway, I’m sure many people could say that about their own religious tradition – whatever it is. And, second, it’s possible to follow the gospel message without actually believing in Christianity or the divinity of Jesus. For example, Thomas Jefferson and Benjamin Franklin saw Jesus as a very good teacher, but questioned his divinity. Jefferson dismissed all the New Testament miracles as fiction. I wonder if Jefferson thought the miracles were inserted into the New Testament to get ‘primitive minds’ to pay attention to the message.

As you can see, I’m just not that impressed with DonExodus’ argument for Christianity. Like I said earlier, maybe we all have our own little pet-ideas that don’t get the harsh light of reason shined on them. Nevertheless, you can go check out his Evolution videos here.

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Where is the Love?

I just found this amusing. Some of the categories on his poster just confuse me though. “Computer Freaks”? I’m not even sure what “Ankle Biters” are. None of the definitions in UrbanDictionary make sense. Maybe he really hates small dogs? Does he just hate the “Child Molesting Homosexuals”, or all Child Molesters?

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