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Archive for the ‘Evolution’ Category

Okay, not really. But, that’s what Al-Jazeera is saying:

“Ardi Refutes Darwin’s Theory,” Al Jazeera announced, in an Oct. 3 article not available on the English version of the website. “American scientists have presented evidence that Darwin’s theory of evolution was wrong,” the article opened. “The team announced yesterday that Ardi’s discovery proves that humans did not evolve from ancestors that resemble chimpanzees, which refutes the longstanding assumption that humans evolved from monkeys.” (Source)

For some real news, here’s a 90 minute video on Ardipithecus, a primate ancestor that predates Lucy by 1.2 million years.

[Thanks: AtheistMedia blog]

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All text taken directly from online Christian fundamentalist forums.

“I can sum it up in three words: Evolution is a lie.”

“You know, there are a lot of things in life that I’ve concluded to be wrong without studying them in depth. Evolution is one of them. You know, the fact that I don’t think about it doesn’t bother me in the least.”

Fundies say the darndest things.

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Want to hear something depressing? Type this into google: “humans apes 46 48 chromosomes”. If you’re knowledgeable about biology, you know that humans have 46 chromosomes, while gorillas, chimps and orangutans have 48. Further, human chromosome #2 looks very much like two chromosomes have fused together into one — neatly explaining where the “missing” chromosome went – and revealing that at one time humans had a chromosome layout just like our ape ancestors. It’s pretty darn good evidence for common descent. (Here’s a video by Ken Miller explaining it.)

But, what happens when you type those terms into google? You get these results:
1. (Young Earth Creationist) Answers in Genesis: A Tale of Two Chromosomes (Oddly, the page is blank, but the internet archive has a copy.)
2. (Creationist) Does anyone remember when humans had 48 chromosomes ? – Yahoo! Answers
3. (Neutral) Chromosome – Wikipedia, the free encyclopedia
4. (Pro-Evolution) Apes vs Human Chromosome Relationship
5. (Intelligent Design) And the Miller Told His Tale: Ken Miller’s Cold (Chromosomal …
6. (Intelligent Design) Evolution News & Views: And the Miller Told His Tale: Ken Miller’s …
7. (Blocked Access; You have to pay to read the article) Orthologous numbering of great ape and human chromosomes is …
8. (Pro-Evolution) Do all Primates (except humans) have 48 Chromosomes? – Evolution …
9. (Pro-Evolution powerpoint) Fusion Event
10. (Pro-Evolution powerpoint) Evolution: Part 2

Creationist spin controls the highest ranked articles, and the pro-evolution articles in the top eight do a poor job of explaining this as evidence for evolution to the common reader. It’s dismal, especially when evolutionists definitely have this nailed as evidence for evolution. I’d much rather see articles like this at the top. My guess is that google is favoring the most recent articles over earlier ones.

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There’s a article up on NewScientist about the Discovery Institute’s new attack on evolution / materialism. They’re apparently going to push the “the mind can’t be explained as a product of the brain” idea to advocate dualism:

“YOU cannot overestimate,” thundered psychiatrist Jeffrey Schwartz, “how threatened the scientific establishment is by the fact that it now looks like the materialist paradigm is genuinely breaking down. You’re gonna hear a lot in the next calendar year about… how Darwin’s explanation of how human intelligence arose is the only scientific way of doing it… I’m asking us as a world community to go out there and tell the scientific establishment, enough is enough! Materialism needs to start fading away and non-materialist causation needs to be understood as part of natural reality.”

Schwartz and Beauregard are part of a growing “non-material neuroscience” movement. They are attempting to resurrect Cartesian dualism – the idea that brain and mind are two fundamentally different kinds of things, material and immaterial – in the hope that it will make room in science both for supernatural forces and for a soul. The two have signed the “Scientific dissent from Darwinism” petition, spearheaded by the Seattle-based Discovery Institute, headquarters of the intelligent design movement… According to proponents of ID, the “hard problem” of consciousness – how our subjective experiences arise from the objective world of neurons – is the Achilles heel not just of Darwinism but of scientific materialism.
(Source)

This is more an attack on materialism than it is evolution. But, the Discovery Institute’s charter isn’t against evolution, exactly – it’s against the idea non-supernatural explanations. I especially liked, “I’m asking us as a world community to go out there and tell the scientific establishment, enough is enough!” – uh, yeah. Everyone who knows virtually nothing about the brain needs to get out there and tell the experts what to believe. Up next: I’m asking the world community to go out there and tell the chemists that their periodic table is a load of crap!

And the two neuroscientists who they’ve enlisted in this fight follow a familiar pattern: people with degrees (i.e. credibility) saying incredibly stupid things – like Egnor’s ridiculous claim that if naturalistic evolution was true, then brain cancer should result in evolving a better brain:

Cancer is a test of Darwin’s theory. Cancer is real biological evolution by random mutation and natural selection, writ fast… Perhaps Dr. Novella has data that show real evolutionary improvements in the brain caused by brain tumors. If he has, he should show us… I’ve never seen cancer make a brain better.
(Source)

Read the full NewScientist article here.

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Sexy Cancer in Fish

Some people think that evolution is all about progress and improvement. I’ve even heard the ridiculous argument that if evolution is true, then mankind should reach moral perfection (showing just how out of touch people’s ideas about evolution are). But, really it’s about differential reproductive success – which is somewhat correlated with “objective” physical improvement, but not always. The Loom has an interesting article about a species of fish where cancer is widespread. This cancer kills the fish before they live their full natural lifespan. And, apparently, certain genotypes are prone to this cancer. So, why hasn’t evolution wiped-out the cancer-prone genotypes? It seems that this particular cancer has a side effect: it makes males very sexy to the females of the species. As a result, the cancer-prone genotype proliferated and this species of fish is prone to this type of cancer.

Fish B: definitely a lot more sexy that Fish A, thanks to that dark tumor in its tail.

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Someone claiming to be “a good Christian woman” setup an anti-spore website, subtitled:

Resisting EA’s War on Creationism

Where she says thing like:

Yesterday I found out about a new game called Spore when my son asked me to buy it for him. It looked innocent enough at first and has “E for Everyone” ESRB rating. But don’t be mislead, apparently “everyone” means everyone they want to teach evolution to.

This entire game is propaganda aimed directly at our children to teach them evolution instead of creationism, or “intelligent design” if you go for stupid PC terms.

The object of the game is to evolve from a “spore” into demon-like intelligent space creatures that violently take over the galaxy.

I created this blog to find support for and follow my progress in letting Electronic Arts know that their biggest attack on Christian values to date will not be tolerated. We can not allow the gaming industry to invade our homes and poison the minds of our children. After all, their billions in revenue and all the advertising in the world are no match for the power of God.

God did not create us through trial and error. He did not make millions of mistakes until deciding on the final concept. Each of his concepts were perfect on the first try.

And 8,500 employees at Electronic Arts to corrupt a child’s mind.

8,500 people all working together and not a single one with enough Jesus to stand up and say what they are doing is wrong.

It makes me sick.

I’m leaning towards this being a prank. Although, most parodies try to be a little more extreme – signaling that it’s a little tongue-in-cheek. But Poe’s Law, you know? Was this done inside Electronic Arts as guerrilla marketing? Is it a prankster doing a parody of Christian fundamentalists? Or a real, sincere person? The pictures and videos of sexually-suggestive Spore creatures makes me think it’s not a real, sincere Christian. They would object to those things, of course, but I just doubt that they would put them up on the website.

Also, whoever it is, they were smart enough to hide their identity using “Domains By Proxy” in the domain registration, and smart enough to put ads in the sidebar of the website. The domain wasn’t registered until September 8 (one day after Spore’s release). Maybe it’s just a savy computer person hoping to make a few bucks on ads while doing a parody that would attract a lot of attention. Opinions?

Update (Sept 12): Yup, it’s a hoax. In this post, the anti-spore creator writes:

But the Bible teaches us that God was not done with man. For we were His creation and He then spoke to Noah in Genesis 8:21-27 after the flood.

“21. The LORD smelled the pleasing aroma and said in his heart: “Never again will I curse the ground because of man, even though every inclination of his heart is evil from childhood. And never gonna give you up. 22. “Never gonna let you down.” 23.”Never gonna run around and desert you.” 24. “Never gonna make you cry.” 25. “Never gonna say goodbye.” 26. “Never gonna tell a lie and hurt you.” 27.”Never truly believe anything you read on the Internet. There will always be cases of Poe’s Law.”

Weird. I had no idea Rick Astley was quoting the Bible. 🙂

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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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