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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.
(Source)

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!
(Source)

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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Lovely.

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’.”

Additionally:

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.
(Source)

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…
(Source)

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