Category Archives: Science

Entertainment, History, Paleontology, Science

The New Mexico Museum of Natural History and Science

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I volunteer at the New Mexico Museum of Natural History and Science, which was created in 1986 and is made up of two floors of exhibits. There are several different halls to the museum, some change over time, but the main thrust of the museum is found in eight halls that make up the Walk Through Time. This section of the museum focuses on the geological history of New Mexico from Precambrian to the present. The exhibits in the halls may change, but the overall theme of them stays the same.

In this blog post, I am going to give a general overview of the museum by describing the eight main halls that make up Walk Through Time. I will provide the map of the museum so one will be able to follow along while reading this post. In addition, this post is the beginning of several posts I will be doing about the museum. Some will be about specific halls, while others will be about specific exhibits found in the halls. This post will always be referenced, thus one will know exactly which part of the museum I discuss in the future.

Walk Through Time starts on the second floor and works its way back down to the first floor.

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Hall One: Origins

In this hall, one is given a brief overview of the formation of the earth and how life might have started. It covers the Precambrian and Paleozoic periods of the earth. Walking farther into this hall one is shown fossils of some of the first life forms on earth and modern creatures that resemble that life. This hall also briefly covers the origin of land-based life. At the end of this hall is the beginning of the major theme of this museum, and that is the natural history of New Mexico. There are fossils, displays, and murals that cover what New Mexico was like at the end of the Paleozoic and beginning of the Mesozoic.

Hall Two: Dawn of the Dinosaurs

In this hall, the first thing you see is a wall talking about the largest extinction event in earth’s history. Next to that, they show what the oceans looked like (with fossils and art) in the Paleozoic and compare with what it looked like in the Mesozoic. The beginning of the hall deals with the early Triassic and has displays of living fossils featuring lungfish (including a live specimen) and coelacanth. Phytosaurs and Placerias, which made up the bulk of the land base life forms during the late Triassic, dominate the late Triassic part of the hall. This hall also includes a display of the earliest mammal (Adelobasileus) and talks about how exactly scientists are able to classify mammals using their ear bones. This hall also includes an exhibit on Coelophysis, New Mexico’s state fossil.

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Hall Three: Age of Super Giants

In this hall, some of the largest dinosaurs to ever live are displayed. This hall is about the Jurassic, which is the period that dinosaurs truly became the dominant animal on the planet. Two of the dinosaurs on display in this hall are Seismosaurus, the longest dinosaur to ever be discovered, and Saurophaganax, the largest carnivorous dinosaur of the Jurassic.

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There is also a display showing the evolution of birds from dinosaurs. It compares the anatomy of Archaeopteryx with that of a pterosaur, a small dinosaur, and one of the first true birds in order to show the homology between the bird/dinosaur and dissimilarity between bird/dinosaur and the pterosaur.

Hall Four: New Mexico’s Seacoast

In this hall, one is able to find a display that shows the movement of the sea that once covered most of New Mexico for all of the Cretaceous period. Because of this sea, the Cretaceous period is one of the most fossiliferous periods in the whole state. When first walking into this hall, one sees into the bottom floor, which has a mosasaur sculpture surrounded by blue floors and walls, representing the sea that covered the state. Next to that is a coastal jungle, which is filled with fossils and sculptures of the creatures that once inhabited the coastal region of the inland sea. One walks down a ramp passed other fossil displays and the coastal jungle. When walking into the first floor one comes into a room entitled “A Bad Day in the Cretaceous”, which shows a film projected on the wall of a meteor striking the earth. Once one leaves this area one walks closer to the mosasaur display.

Hall Five: Volcanoes

In this hall, one is treated to a walk through a generic volcano. New Mexico has more extinct volcanoes than any other state. Inside this hall, it discusses all four different types of volcanoes and the lava they produce. It also shows examples of all four volcanoes with ones found in New Mexico. This hall has been here, virtually unchanged since the museum opened in 1986 and is still one of my favorites along with most of the people that visit.

Hall Six: Rise of the Recent

In this hall, one is able to see a brief overview of much of the Cenozoic of New Mexico. This hall contains some of the most beautiful murals in the whole museum. The best mural in this hall is the mural showing the evolution of the horse. There are a few fossil exhibits found in this hall including Diatryma, which was discovered here in New Mexico by Edward Drinker Cope.

 

Hall Seven: Cave

In this hall, an artificial cave is created to show all the different aspects of caves. There are different displays that light up and tell one about the different formations found in caves. This exhibit also discusses the life forms that one would find in a cave. In addition, a display talks about Carlsbad Caverns, which in my opinion is the most beautiful cave system on earth.

Hall Eight: New Mexico’s Ice Age.

In this hall, there are several different displays of the different animals found in New Mexico during the Pleistocene. This hall includes erected skeletons of a Columbian mammoth, two dire wolves, and a saber-toothed cat. It also has a mural, which depicts how lush New Mexico would have been during the ice age. This is also the only hall that contains depictions of human activities in the Museum, which is a mural of the Clovis People butchering a Columbian Mammoth.

Edited by Dean, 11/04/2013
Reason for edit: Spelling/word-choice alterations, all images but the first reduced in size by 50%.

News, Science

The ENCODE delusion

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A few months ago, I wrote a post about junk DNA and ENCODE. Since then, more evidence has surfaced so I’ve decided to make this into a blog post. I’ve slightly modified the original post as well as added the new information plus all the relevant links. This is a long and sometimes technical post. Note: “Creationist” is interchangeable with ID-proponent. They’re the same.

 

The main problem with this story is not what scientists have claimed and then found, but rather what the popular press has (mis)understood. This is also a story about scientists failing to communicate science properly. AronRa said on the 31st of May, 2009, in his video Ida Know (the first of a five-part summary about the 47-million year old primate fossil Ida) the following, which also holds true about this story:

But sadly, the media isn’t entirely to blame, some of this has been done by scientists.

…

It is highly inappropriate sensationalism and the way it’s described is very misleading to anybody who doesn’t understand taxonomy very well and almost nobody does.

The same is true in this case, only substitute “taxonomy” with “evolution”, “genetics” and “biochemistry”.
A pop-science journal Arstechnica (Author John Timmer) has also commented on this phenomenon:

ArsTechnica: Most of what you read was wrong: how press releases rewrote scientific history

Many press reports that resulted [from the ENCODE release] painted an entirely fictitious history of biology’s past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can’t entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work,and, in some cases, the scientists themselves.

…

Unfortunately, things like well-established facts make for a lousy story. So instead, the press has often turned to myths, aided and abetted by the university press offices and scientists that should have been helping to make sure they produced an accurate story.

I’ll go into the details of the ENCODE story near the end, but first we need a short history of “Junk DNA”.

A history of “junk DNA”

The story begins with Susumu Ohno. In 1970, he wrote a book (Ohno, 1970a ) in which he laid out the argument for the role of gene duplication in evolution. We now know that it does indeed play its part. One thought experiment he had regarded genes that were duplicated (in his example, three sequences sharing the same sequence) and not under pressure by selection any more. If there is no selective pressure, they would mutate and two out of three would likely serve no function, due to high mutation rates.

Ohno 1970a, p.62

[It is likely that] in a relatively short time, two of the three duplicates would join the ranks of ‘garbage DNA’.

This was the first time anything like this was proposed. Only two years later, in another paper (Ohno, 1972) would he coin the phrase “junk DNA”. So what was “junk DNA” or “garbage DNA” to him? Well it’s based on a very well-known observation:

Ohno 1972

If we take the simplistic assumption that the number of genes contained is proportional to the genome size, we would have to conclude that 3 million or so genes are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own.

As we now know, we have roughly 20,000 genes, which fit well with Ohno’s prediction of no more than 30,000 genes. It was also observed that there can be a lot of duplications and insertion of retroposons without affecting the body in any way. I talk about this later on, under the heading “pseudogenes”.

At the time of Ohno’s writing, “junk DNA” was “meant to describe the loss of protein-coding function by deactivated gene duplicates, which in turn were believed to constitute the bulk of eukaryotic genomes”. (Genomicron, 2007)

A very important part follows:

As different types of non-coding DNA were identified, the concept of gene duplication as their source, and therefore “junk DNA” as their descriptor, found new and broader application. However, it is now clear that most non-coding DNA is not produced by this mechanism, and is therefore not accurately described as “junk” in the original sense.

So in the original sense, we don’t have a lot of “junk DNA” after all. The important thing to know here is that the term has been butchered by the media to mean all non-coding DNA, which strictly shouldn’t be called “junk DNA” but rather “pseudogene”, coined in 1977 (Jacq et al. 1977) to describe a functionless gene. Now note the miscommunication: There is a difference between “junk” (stuff one keeps) and “trash” (stuff one throws out). This was noted in 1988:

Brenner 1998

There is the rubbish we keep, which is junk, and the rubbish we throw away, which is garbage.

And in 1990, Brenner said the following:

(S. Brenner, The human genome: the nature of the enterprise (in: Human Genetic Information: Science, Law and Ethics, No. 149: Science, Law and Ethics, Symposium Proceedings (CIBA Foundation Symposia) John Wiley and Sons Ltd 1990, Source) <– One problem with that blog post is that much of it is wrong. I merely provide the source to show where I got the picture from.

And even in 1973, Ohno suggested a potential function for “junk DNA”:

Ohno, 1973

The bulk of functionless DNA in the mammalian genome may serve as a damper to give a reasonably long cell generation time (12 hours or so instead of several minutes)

 

Genomicron, 2007

From the very beginning, the concept of “junk DNA” has implied non-functionality with regards to protein-coding, but left open the question of sequence-independent impacts (perhaps even functions) at the cellular level. “Junk DNA” may now be taken to imply total non-function and is rightly considered problematic for that reason, but no such tacit assumption was present in the term when it was coined.

Gregory goes on to make a very astute observation: If there is no function for all genes, creationists are in serious trouble. (Note: Recent reading of a creationist blog post suggests that there is at least one creationist who does not adhere to this and thinks it wouldn’t matter much if their prediction weren’t true. I’ve yet to find the original source [a guy called Axe?] so I’m left to wonder how that should work… This doesn’t detract from the point that most creationists do hold the view presented both above and below.)

Genomicron, 2007

[This is why] all non-coding DNA must, a priori, be functional.

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith’s (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that “eukaryotic non-coding DNA is functional”. The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.

Apart from the above mentioned potential function for “junk DNA”, many more have been identified since:

Genomicron, 2007

Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

In addition, I believe one can add both Epigenetics and Evo-Devo to that list.

Finally, Genomicron notes the following:

Genomicron, 2007

More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.

Pseudogenes

Now I need to explain pseudogenes. I think the easiest way is to use this picture from the wikipedia article, which I modified for the purpose of illustration:

As you may know, amino acids are encoded by reading DNA sequences in triplets. If, as in the above sequence, an insertion, deletion and point mutation occurs, the triplets are read differently. The results in amino acid encoding are shown above. If the new sequences produce premature stop-codons or, as in this case, simply different amino acids, genes may not be activated and proteins may not be produced. Sometimes they are encoded but do not actively help the organism.
These are then called pseudogenes.

The ENCODE delusion

A few months ago, the ENCODE staff published some research, which prompted the following statement by the EFF:

EFF

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California’s warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

But as I showed above, functions for “junk DNA” have been known since before the term was even coined! This is what I’m talking about when criticizing the way scientists convey science and the way newspapers bring it to the public. (Luckily, some scientists have spoken out against the ENCODE fiasco. And hey, even some folk from the ID-crowd.)

But let’s back up a little. ENCODE has been working for quite some time now and, as you would expect, it has been talked about since at least 2007. (Arthur Hunt on Panda’s Thumb, 2007) Even then, Creationists wanted to claim what they claim now, namely that all DNA has a definite function. There was (at least) one problem for them: A 2005 paper (Wyers et al. 2005) showed that “much of the RNA made by a cell is thrown away. This includes RNA encoded by intergenic regions.” (Quote from Arthur Hunt, 2007)

PZ Myers documents a second story, with a 2010 paper (van Bakel et al. 2010) explaining once again that genes only make up about 2% of the genome, while the rest is non-coding.

That takes us back to the 2012 report from ENCODE. They claimed that 80% of the genome serves some biochemical function, with “function” being defined as participating “in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type”. That’s where the real problem in communication lies: The definition of the word “function”.

PZ Myers

That isn’t function. That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.

I’ll try to make this as clear as possible, so I’ll draw on an analogy. Imagine you found two ball-point pens. One of them is a normal pen, the other lacks the ball-point. The first pen has a definite function: To write. The second one may have other functions (like removing ear-wax from your ear), but that’s not a definition of function any sane person would recognize.
The same happened to ENCODE: The way they define “function” is so broad that it’s absolutely useless. Indeed, much randomly generated DNA can be said to have “function” under this definition.

Also note that in his blog, Ewan Birney (kind of) explains what “function” means in ENCODE terms. What’s noticeable is that it could just as well have been swapped for “specific biochemical activity”, which takes the wind out of the sails completely.
In another Q&A point, he said that using the 80% number instead of the 20% functional bases (notice a difference?) was used to… hype up the story. That’s basically it.

Ewan Birney, Q&A

Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader, they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

And again from Arstechnica:

So even as the [2007] paper was released, we already knew the ENCODE definition of “functional impact” was, at best, broad to the point of being meaningless. At worst, it was actively misleading.

…

In the lead paper of a series of 30 released this week, the ENCODE team decided to redefine “functional.” Instead of RNA, its new definition was more DNA focused, and included sequences that display “a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).” In other words, if a protein sticks there or the DNA isn’t packaged too tightly to be used, then it was functional.

That definition nicely encompasses the valuable regulatory DNA, which controls nearby genes through the proteins that stick to it. But,and this is critical,it also encompasses junk DNA. Viruses and transposons have regulatory DNA to ensure they’re active; genes can pick up mutations in their coding sequence that leave their regulatory DNA intact. In short, junk DNA would be expected to include some regulatory DNA, and thus appear functional by ENCODE’s definition.

…

The ENCODE team itself bears a particular responsibility here. The scientists themselves should have known what the most critical part of the story was,the definition of “functional” and all the nuance and caveats involved in that,and made sure the press officers understood it. Those press officers knew they would play a key role in shaping the resulting coverage, and should have made sure they got this right. The team has now failed to do this twice.

All that being said, Sandwalk notes two things:

1) The word the ENCODE-people are looking for is not “function”, it’s “noise“.

2) The debate isn’t only about the definition of “function”, but something deeper. An additional problem may be that some scientists don’t understand evolution. That’s pretty sad in this day and age.

 

A further update comes from a 2013 paper in “Genome Biology and Evolution”. The paper is discussed over at Pharyngula and it basically rips into ENCODE’s papers. There’s a lot of technical stuff I needn’t cover, so I’ll limit myself to mentioning one thing: Other researchers have found only 10% true functionality, that’s 70% less than the folk over at ENCODE.

I’ll conclude:

1) “Junk” DNA was, from the moment of its conception, a misnomer. Just like “Big Bang” falsely conjures the image of an explosion, “junk DNA” falsely conjures the image of complete non-function or garbage. However, in both cases that’s not consistent with what scientists have been saying even before the term was coined. “Junk DNA” should not be in common usage. A more precise term would be “pseudogene”.

2) Conveying what “junk DNA”, non-coding DNA and pseudogenes are, as well as the nuanced differences between the terms, is a difficult job. Sadly, neither scientists nor journalists have done a good job of explaining the terms. It would be interesting to make an extremely careful and detailed YT series on this subject.

3) Much of the ENCODE hype rests on the definition of the term “function”. If the general public and creationists were aware of what “function” means in ENCODE terms, the hype would almost completely fade away. Note that I’m not saying that the results were wrong, inconclusive or not worthy of recognition, I’m simply saying that they were over-hyped. (Which would put them into the second circle of scientific hell!)

4) This problem also creates an opportunity. We now understand what we did wrong and this may encourage scientists to be more careful in the future when explaining things. I hope to make a blog series on the public understanding of science soon and this will be one of my focuses.

Below are all the references used in the creation of this post. The first one is only scientific papers, the second one is blog posts and opinion pieces.
All references with links attached are the resources I used myself, other resources in plain black are additional resources.

References

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Batten, D. 1998. ‘Junk’ DNA (again). Creation Ex Nihilo Technical Journal 12: 5.

Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes. Proceedings of the Royal Society of London, Series B 266: 2053-2059.

Bejerano, G., M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, and D. Haussler. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.

Bennett, M.D. 1982. Nucleotypic basis of the spatial ordering of chromosomes in eukaryotes and the implications of the order for genome evolution and phenotypic variation. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 239-261. Academic Press, New York.

Bergman, J. 2001. The functions of introns: from junk DNA to designed DNA. Perspectives on Science and Christian Faith 53: 170-178.

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Bostock, C. 1971. Repetitious DNA. Advances in Cell Biology 2: 153-223.

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Jerlstrà¶m, P. 2000. Pseudogenes: are they non-functional? Creation Ex Nihilo Technical Journal 14: 15.

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Ohno, S. 1973. Evolutional reason for having so much junk DNA. In Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man (ed. R.A. Pfeiffer), pp. 169-173. F.K. Schattauer Verlag, Stuttgart, Germany.

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Patrushev, L.I. and I.G. Minkevich. 2006. Eukaryotic noncoding DNA sequences provide genes with an additional protection against chemical mutagens. Russian Journal of Bioorganic Chemistry 32: 1068-1620.

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Slack, F.J. 2006. Regulatory RNAs and the demise of ‘junk’ DNA. Genome Biology 7: 328.

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Wieland, C. 1994. Junk moves up in the world. Creation Ex Nihilo Technical Journal 8: 125.

Williams DL, Slayden RA, Amin A, et al. 2009. “Implications of high level pseudogene transcription in Mycobacterium leprae”. BMC Genomics 10: 397.

Woodmorappe, J. 2000. Are pseudogenes ‘shared mistakes’ between primate genomes? Creation Ex Nihilo Technical Journal 14: 55-71.

Woolfe, A., M. Goodson, D.K. Goode, P. Snell, G.K. McEwen, T. Vavouri, S.F. Smith, P. North, H. Callaway, K. Kelly, K. Walter, I. Abnizova, W. Gilks, Y.J.K. Edwards, J.E. Cooke, and G. Elgar. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biology 3: e7.

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-37

Yunis, J.J. and W.G. Yasmineh. 1971. Heterochromatin, satellite DNA, and cell function. Science174: 1200-1209.

Zuckerkandl, E. 1976. Gene control in eukaryotes and the C-value paradox: “Excess” DNA as an impediment to transcription of coding sequences. Journal of Molecular Evolution 9: 73-104.

Zuckerkandl, E. and W. Hennig. 1995. Tracking heterochromatin. Chromosoma 104: 75-83.

Zuckerkandl, E. 1997. Junk DNA and sectorial gene expression. Gene 205: 323-343.

 

References from pop-science resources

Gregory, T. R. 2007. Genomicron Junk DNA summary

Genomicron ENCODE reply

Brenner, S. 1998. Refuge of spandrels. Current Biology 8: R669.

Talk Origins summary

Talk Origins claim CB 130

Pandas Thum: Junk DNA

Possibly slightly misleading article at ScientificAmerican on Junk DNA <— Read this one only after you’ve read the other ones plus my summary, otherwise you might be a bit confused!

Sandwalk has many more articles on the topic. They’re not a must-read, though, merely more information on the same.

Findandpea have another great review of the way the media failed to report properly on this. But again, scientists fell for it too, so reporters are not exclusively to blame.

Finally, Genomicron maintains an updated list of posts on the topic over at his blog. In case you’re missing anything, it can either be found at Sandwalk or at Genomicron.

Medicine, Science

The great vaccination scare

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Most of you will have heard of the MMR vaccine controversy. A man, Dr. Wakefield, suggested that the MMR vaccination increased the likelihood of autism in infants and children. People stopped vaccinating their kids, which resulted in a few thousand cases and a few deaths. All of them could have been avoided, had it not been for Dr. Wakefield.

As we know, people don’t learn from their mistakes, the deep-rooted fear still possesses them. In a previous blog entry, I talked about my homeopath/M.D. aunt, among other things. She’s a lot of things I could make fun of, but one of the things that makes me sad is that she also opposes vaccines. She went to Kenya without a single vaccination, even though yellow fever is a deadly disease. Her whole family is the same, they all oppose vaccinations.
Recently, I talked to a friend of mine. She’s also against vaccinations, because they can “harm your immune system”.

Let’s look at anti-vaccers claims:

Vaccines are not effective, vaccines are not safe, vaccines are not moral or vaccines are against my religion.

We can dismiss the last two claims out of hand. If you don’t want to use them due to your religion then your religion is pretty fucked up.
I also reject the case for personal liberty. If your idiocy is putting other people at risk, you have no say. Period. Your rights should be stripped away to protect the rest of the population.

So we’re left with two questions:

1) Are vaccines effective?

2) Are vaccines safe?

The efficacy-question is easily answered: Vaccines are among the few things to come out of the pharma-industry that are so very obviously effective that we shouldn’t even have to think about this.

Forbes recently posted a short article on the topic. The following info-graphic was compiled from a recent article, linked in the Forbes-post.

Vaccines Info-graphic

Smallpox was once one of the most prolific killers, with an estimated 300-500 million killed just from Smallpox alone. And now, it’s virtually eradicated.

Thanks to vaccines? I think the above is ample evidence to that extent, but there’s more. The following graphic (Wikipedia) was compiled for the prevalence of rubella, but it could equally have been compiled for any other vaccine. It always follows the same path: A vaccine is introduced and given, the prevalence of the disease goes down.

Prevalence of rubella

 

So on to the second argument: Safety.

When I was a baby, I was immunized against MMR. The batch I received was tainted, I fell ill. I could have died, but was given medication and survived. But even in the best of circumstances, people can have adverse reactions to the immunizations.

Here’s the deal though: These reactions are incredibly unlikely to happen.
A paper from a  few years ago discussed this and came up with the following conclusion: “[T]he expressed doubts about the safety of vaccines are unjustified.”
That’s it really. Vaccines are an effective and safe way to counter several potentially deadly diseases. To eradicate these diseases, we all need to take the vaccines. If you don’t immunize yourself, you not only put yourself at risk but also the rest of the population, by allowing the disease to survive.

I don’t think any argument can be made that vaccinations are dangerous or ineffective. If you think there is, please, I need a laugh right about now.

Medicine, Research, Science

Evidence-based medicine: Introduction Part 1

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In my last post, “What’s the harm?”, I talked about the problems of taking medicine (or treatments!) that’s neither good nor bad for you. I also talked about “evidence-based medicine”, but didn’t really delve into that topic. I won’t do that in this post, either!

So what, you may well ask, do I want to talk about now? I want to give you a look into what a few doctors do and why their approach is deeply flawed. I’ll give one specific and not-well-known example of alternative medicine as well as some obstacles I found when investigating its efficacy.

In short, I’ll talk about why medicine needs evidence and why practitioners of alternative medicine might be reluctant to look for evidence. I apologise if the post is fairly long, but I need to flesh out my example to make sure you understand the practices behind it.

 

First, let me try to explain PsychoSomatic Energetics (PSE).

Watch this video. Read this page. (If you speak German, read this book. Or don’t, it costs money… Twenty pages are also available here.)

Done? Now what do you know about PSE? Not very much, I’d think. You know it has something to do with “energy blocks” and with measuring the “subtle energy field”. But how does it work?

Here’s where I come in. I’ve read the book and I’ve talked not only to people who’ve taken a seminar in PSE, meaning they’re qualified to test with it, but I’ve also E-Mailed one of the inventors of PSE, the ex-Wife of the guy in the video. What I will now lay out will sound confusing, mad even. If you don’t trust me, read the book and cross-check what I’ve said. If anything I’ve said sounds exaggerated or false, feel free to criticize me in the comments.

PSE is based on Freud’s psychoanalysis, basically issues from the past are said to influence your current health. In Freud’s case, that meant mental health, in PSE language mental health influences physical health. Up until now, the theory’s sound. Of course depressions and other mental problems can affect the body, but the effects can be hard to spot and even harder to treat.  That’s why psychotherapy is such a difficult field, why so many therapists have to take long vacations and why they are given the harshest, yet most self-preserving advice.*

Here, then, is PSE’s amazing promise: Not only can we find out what is wrong, and how much is wrong, but we’ll even be able to cure them in a relatively short time using homeopathic remedies. Now we haven’t yet looked into homeopathy, so we’ll assume for now that the remedies are 100% effective. That’s how generous I have to be just to take PSE seriously. So what should strike us about the above is this: It claims to cure all energy-related problems. Any remedy that claims to cure everything of anything can be almost immediately dismissed.

Now I’ve failed to tell you two things:
1) What does PSE supposedly treat? “Energy problems” is not very specific a term in this context. I’d refer you to Dr. Banis’ book, but that’s not very helpful: “Most illnesses are caused by blockades of the soul, which can’t be tested nor treated early enough. That’s what we try to counter with PSE.” If you found that illuminating: Congratulations, you’re smarter than I am.
I have talked to some people though, and their answer is the same: “Almost everything can be treated with PSE, if it’s found early enough”. I’ll be generous and say “Non-serious mental problems (slight depressions, slumps, feeling worn-out, etc.) and small boo-boos (coughs, “feeling unwell”, etc.) can be treated”.

2) What is energy and how does it relate to PSE?
Remember that PSE is bound to eastern traditional medicine. In that tradition, the body has “energy” and that energy is located in one of the seven “chakra-points”. That energy is generally an astral “energy”, a sort of “I’m full of energy”-thing, but recent attempts (Deepak Chopra et al.) have tried to make this “energy” a real energy, a physical force.
If you read the PSE-book I’ve referenced above, you can find at least three definitions of energy:
a) The above described astral energy
b) Magnetism, in this case the slight magnetic field around the body.
c) The energy we know from physics known as “force” and the energy we know from electricity known as “electric charge”.

According to PSE, we can measure the energy at every chakra-point on a scale from 1-100, with every one of those points further being divided into four “energies” known as “vital”, “emotional”, “mental” and “causal”. We don’t  need to understand them, we just need to know that according to PSE, if any one of those energies suffers (note: that’s 28 different measurements!) then we won’t have enough energy, which can either result in us feeling depleted (think of it as forgetting to turn off a light at home, it drains your money) or in us becoming sick (a light bulb pops due to it being overused). I won’t go to tell you that it’s then compared to the four “juices” of the body, also known as the “four temperaments“. That would just be mean and discredit the whole thing immediately.

In any case, back to PSE. Now that we’ve understood what is to be tested, we can see how it is tested. The process is relatively simple:

Take a machine, in this case the Reba® special test device and hook the patient up to it. You do that by placing the machine on a flat surface, lying the patient down next to them and attach a wristband to one of their wrists.
Next, you take an vial of the homeopathic remedy you want to test (one vial corresponds to one of the 28 levels I described above) and place it into the receptor of the machine. Note that at no point does the actual remedy get into contact with the device.
Having done that, you switch on the machine and test for the first of five levels. (100/5=20, so you test at 20, then 40, then 60, etc.) To do that, you (being the doctor) take the arms of your patients and lightly pull on them. (Arms outstretched behind/above your head) If one arm is longer than the other one (supposedly called “kinesiological arm-length reflex”), you know that energy is lacking.

Practical example: If you test vial one and your patients arms are the same length at 20, but one is shorter at 40, then you write down “20”, because that’s the “available energy level”. If they’re the same length at 20 and 40, but different at 60, you write down 40. And so on.

And that’s it, basically. You repeat that 28 times and write down the results. If they’ve got energy level 100 everywhere save for vial 28 (associated with “wrong thinking”), you give them remedy 28 to “boost their energy level” at that point. After six to twelve months, the patients come back and if they tell you that they feel better, then everything’s fine. If they don’t, you re-test them and give them more remedies.

Now obviously, there’s so much wrong with that, I won’t be able to go into all. A quick overview:

  • What is energy and why do they use so many different, conflicting definitions?
  • How can PSE supposedly treat “everything”?
  • How can we test if “chakra-points” really exist?
  • Why are they using outdated concepts like the “four-temperament” theory?
  • How does the test device work?
  • Is the arm-reflex reliable? (Hint: NO!)
  • Isn’t the whole thing a bit subjective?

But most importantly of all, I want you to focus on one very specific problem: Where’s the evidence that it works? Anybody can say that it works (more on that much later), but how can I prove that it does?

Here’s where PSE encounters some very serious problems. There are four!!! relevant studies to this, with a total sample size of about 2000-2500. That’s not a bad sample size, it should be enough to see if PSE works or not. Below are the four studies:

Schmetterlingsstudie – Butterflystudy

Banis R, Banis U: Psychosomatische Energetik – Ergebnisse einer Praxisstudie. Schweiz Zschr Ganzheitsmed 2004;16:173–178.
Holschuh-Lorang B: Psychosomatische Energetik in der Allgemeinmedizin – Ergebnisse einer Praxisstudie. Schweiz. Zschr. GanzheitsMedizin 2004;18,368–371.
Banis R: Multizentrische Praxisstudie zur Psychosomatischen Energetik. Schweiz Z Ganzheitsmed 2010;22:269–272.

If you look at them, they all document a large percentage of “good” and “very good” results. But didn’t I just tell you PSE had serious problems when it comes to evidence?

Yes, because the above is not evidence of anything. It’s worthless trash, not worth the bits it’s written in.
That may sound harsh, but I’ll explain myself and I hope you’ll share my view.
Take note, because this is what the whole post has been building up to!

Eye-witness testimony is the lowest form of evidence in science, especially so in medicine. You can get better without the medicine or treatment doing anything (placebo effect), you can think you’re getting better even though the evidence shows no benefit and you can think the drug as a whole is beneficial (just not in you) even when it’s actually actively killing people. In his excellent book Bad Pharma, Ben Goldacre documents (pages 140-143) the effects of a drug called Iressa on the general population. Basically, Iressa showed no real-world improvements for patients, yet they gave positive testimonies nonetheless.
So at the very least, we can expect PSE to look slightly beneficial just due to this misinformation or misunderstanding or whatever you would like to call it. We will also expect it to look more beneficial because of the placebo effect and, because often people go to get treated with nothing more than “feeling bad” or “anxiety”, even better because people care for them and talk to them.

None of that would matter if PSE were ever tested fairly, that is to say using real, measurable effects. Since none exist (bar the subjective “I feel well” from patients), we would at the very least expect PSE to be tested against a placebo. After all, we know how potent the placebo effect can be. No, none of that. After over 15 years of PSE having been practised, NOT A SINGLE study has been conducted comparing PSE to a placebo. I even went as far as suggesting a cooperative effort between Dr. Banis and myself, but that failed due to a number of factors. (She was interested and would even cooperate with me, but no suitable venue nor funding was found.)

This is what this post has been about: More than fifteen years of practising PSE have passed and we don’t even know the most basic thing about it: Does it work? (I’d say no, but then you shouldn’t take my word for it.)

So I asked a practitioner (or at least advocate) of PSE about the lack of evidence for PSE, not to mention the various pieces of evidence against PSE. What does she make of that?
Her response: “I don’t care about evidence, I have seen it work with my own eyes. And I probably wouldn’t change my mind if I saw studies to the contrary.”

This staggering lack of curiosity about the evidence is baffling. Why don’t you want to know if it works? Isn’t evidence something to actively seek out? And even if you don’t want to conduct the studies yourself, wouldn’t you at least like to know?
Interestingly, I was then chastised by nearly everybody at the table for daring to challenge a doctor and for being a “damn skeptic”.

So as of today, the evidence is still not in on PSE, but it most definitely is in on homeopathy and since that doesn’t work we can safely assume that PSE doesn’t work either. If new evidence comes along, I’ll review my view and make a second post on this issue.

For now though, I hope you’ve taken one thing away from this: Medicine needs evidence, otherwise we don’t know if something works or not. I’ll give specific examples for that in the next post, this one here was mainly to give one example of practitioners or advocates of alternative medicine being reluctant to seek out evidence against which to measure their medicine or treatment.

Beware of alternative medicine.
*In a lecture, future therapists were told the following: “Some day in the future, a person will walk through your door. This person will be extremely friendly and will immediately open up to you. They’ll tell you that you’re the only person who’s ever understood them and that all previous doctors just couldn’t find the answer but that they just know that you’ll be better. If that ever happens, THROW THEM OUT! They’re lunatics and you can’t help them”. -unsourced

Edited by Dean, 06/03/2013
Reason for edit: Spelling correction [1].

Reason, Science

Of species and kinds

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One familiar argument an evolutionary proponent will encounter when dealing with creationists is the “species problem”. Essentially the argument is that there is not a definitive definition for a species. This almost inevitable argument comes up because the evolutionary proponent asks the creationist if they could define kind. Creationists believe that since biologists cannot come up with a consensus on species that applies to every organism, it gives them a free pass to not define kind.

 

The problem with this argument and the reason we have a “species problem” in biology is that different forms of life reproduce differently. For example, a definition for bacteria will not work for a population of mammals because they reproduce in a different manner. Thus, one is able to produce a robust definition of a species for organisms that reproduce sexually (i.e. reproductive isolation), but have a more fluid definition for species when it comes to asexually reproducing populations.

 

However, this is all beside the point and can be considered a red herring, thus one does not even have to address it. The main issue with this creationist argument is that the definition for kind should be vastly more robust than any definition of species. Young Earth Creationists believe that their God came to Earth, seeded all life on this planet, and made sure that each kind would reproduce after its kind. Thus, if a god(s) truly wanted to do this we would be able to see distinct genetics unique to certain kinds, which are not shared with any other animal outside of their kind. That is, there should be genetics shared only between the cat kind or dog kind that are not found in other organisms and we should not be able to find shared genetics between the two kinds.

 

Nevertheless, this is not what we see when we look into the genetics of life. Every time we look into the genome of an organism, we can see its shared life history with every other living organism on Earth. To date, we have not found a gene sequence unique to a group of organisms except at the species level, and those unique genes are what make that species different. It is this fact that is the real reason creationists refuse to define kind and would rather hide behind the “species problem” when asked to define kind. If the creationists were correct, and god(s) created different kinds then geneticists would be unable to create phylogenetic trees linking all organisms into clades based on their evolutionary history. To make this problem worse, other phylogenetic trees, based on morphology, embryology, etc…, should not be able to produce similar (statistically the same) trees. One would think that their genetics would be different, since all the kinds were created separately with no relation to the other.

 

Thus, the next time a creationist refuses to define kind, kindly remind him that comparative genetics has definitively proven universal common descent and that there have been no genetic markers to indicate that there ever were unique kinds. The “species problem” is not equivalent to the lack of a definition of kind.

Edited by Dean, 25/02/2013
Reason for edit: Minor corrections of grammar & punctuation.

Anthropology, Archaeology, Paleontology, Science

What is a …

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I would like to answer a frequent question I hear while volunteering at the natural history museum. That question is “what is a paleontologist?” I will also throw in archeologist and anthropologist for good measure.

To answer the first question, a paleontologist is a person who studies the history of life on Earth. They are the people that dig up dinosaur fossils and other amazing plants and animals that once lived on our planet. The excavation and curation of the fossils they discover is what gives us our understanding of Earth’s past. There are several subfields of paleontology, which include paleobotany (plant fossils), invertebrate paleontology, and vertebrate paleontology. All of those can also be broken down into more fields.

So what is an archeologist?

An archeologist is a person that studies human prehistory. Archeologists are the people that dig up human remains, artifacts, and animals once preyed upon by humans. Since most of human history happened before anything was written down, archeology is our only look into the vast majority of our history on Earth. There are several subfields of this as well, such as bio-archeology (human remains), zoo-archeology (animal remains), lithic analysis, ceramic analysis. From there the fields are usually broken up into the area of the world you study and the time period you are investigating.

So what is an anthropologist?

An anthropologist is a person that studies primates, everything from lemurs to humans. In fact, in the U.S. archeology is considered a subfield of anthropology (most European countries place archeology into history). The other subfields are biological anthropology (anatomy of mainly humans), ethnology (or cultural anthropology), and human evolutionary ecology.

Now, there is some overlap in all three, but major distinctions between the three as well. for example if you found something you thought might be a fossil, you probably would not want to ask your local archeologist what it is, on that same note, if you discovered a arrowhead, a paleontologist would not know much more than you already know.

However, an example of the overlap is the subfield of anthropology I someday hope to become a part of. That subfield is called paleoanthropology and that is the field that studies the hominins and other ancient primate species. This subfield deals with primates (thus anthropology), which are very old and mostly extinct (thus paleontology) and some of the specimens can be classified as human and were creating lithics (thus archeology).

I hope this short overview of these three scientific fields was helpful and may have cleared up any questions you might have had. If anyone has any questions about any of the three fields, please ask away. I will be more than happy to address any questions.

Science

What’s the harm?

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This will be my first post on alternative medicine. In it, I will try to cover the prominent excuse people give when taking things like homeopathy: “If it doesn’t help me, at least it won’t hurt me”, otherwise known as “what’s the harm?”.

Edzard Ernst, the first Professor of Complementary Medicine (University of Exter) to ever exist, defined complementary and alternative medicine (CAM) as “health care which lies for the most part outside the mainstream of conventional medicine”. Alternative medicine, as defined by nsf.gov, refers to “all treatments that have not been proven effective using scientific methods”.

The opposite of the above two is “evidence-based medicine”, defined as “the conscientious, explicit and judicious use of current best evidence in making decisions about the care of individual patients”. (I’ll take a look at THAT much, much later.)

With the definitions out of the way, let’s look at what proponents of alternative medicine propose, using homeopathy as an example: Proponents of homeopathy are often heard to say that homeopathy has no side effects.*

So, the reasoning goes, if it can’t harm you, you can just take it anyway. (I’ll assume, for the sake of this post, that alternative medicine has no beneficial effects what so ever. I’ll explore this in later posts.)

There are two rebuttals to this:

1) Spending money on alternative treatments can result in you not having money for proper medication. Approximately $34 billion are spent on CAM in the US alone. A direct comparison of a homeopathic fever remedy and ibuprofen showed that the homeopathic remedy cost $7.05, while ibuprofen cost $6.98. That’s not a huge difference and it also doesn’t address whether the homeopathic remedy will actually help against the fever. The difference, $0.07, is negligible, but in favour of the evidence-based treatment.

I might make a later post detailing the cost of the alternative treatment vs the evidence-based treatment, but for now even a cursory look at common treatments shows that “alternative medicine is less expensive than evidence-based medicine” is, at best, misleading.

2) Spending time on alternative treatments can delay access to real treatment.

Bob Marley didn’t allow the amputation of his cancerous toe due to religious reasons and sought out alternative treatments. He died. Former President Warren G. Harding died after his homeopathic practitioner did some weird stuff on him.

In total, What’s the harm? documents around 370,000 deaths, 305,000 injured and nearly $3 billion in economic damages due to pseudo-science, of which surely more than half can be traced back to CAM.

So the next time someone tells you to go to a practitioner of CAM, politely decline, show them the above website and go to a real, licensed doctor. They’re far from perfect, but at least they can do some things right.

 

*It must be noted at this point that any and every remedy, be it a placebo or a real remedy, can have side effects due to the nocebo effect. What is meant is “no side effect due to the active ingredient”.

Future projects on the topic:

In my next post, I’ll look at why studies in medicine are important.
My third post will deal with a few alternative treatments and look at their benefits.
A series of posts sometime in the future will look at evidence-based medicine, what it is and how much evidence there really is.

Anthropology, Archaeology, Introductions, Paleontology, Science

First blog post

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Seeing as how this will be my first blog post, I thought I would start by giving my CV.

I am currently a contract archaeologist; my specialty is human and faunal remains (I am not using that much today). I have been on excavations in Hawaii, Spain, and in my great state of New Mexico. I obtained my Bachelor of Science with honors in Biological Anthropology from the University of New Mexico in 2010. My senior thesis was about dental microwear on extant primate populations (it can also be used to reconstruct paleo-environments). I one day hope to return to school and continue studying skeletal anatomy, paleoecology, and cladistics. I also volunteer at my local natural history museum, which I also hope to obtain a larger role in soon (hopefully specimen preparation work and excavations). To sum it up, I like bones and fossils.

My main Ethernet hobby, as many of you already know from practically all my forum posts, is debunking creationism. With part of this blog, I am hoping to add just a little more firepower to the pro-science side of this argument, not only in biology, but also in all fields that creationism tries to distort and tamper with.

The other part of this blog I am hoping to answer general questions people have about archaeology, anthropology, and paleontology; a basic “ask an archaeologist/anthropologist/paleontologist” blog. I would welcome all questions; the main thrust of my volunteer work is answering questions from the public. Thus, any questions are welcome and will be answered by me (hopefully).

For the most part that is what I would like to blog about; I may blog about other things, such as how great New Mexico is, but look forward to creationism debunking and archeo-babble.

I guess this is enough for my first post. I hope everyone will enjoy my blog as much as I enjoy writing it.

Have a nice day. 🙂

Culture, Literature, Philosophy, Reason, Religion, Science, YouTube

Critique Of Alvin Plantinga’s Evolutionary Argument Against Naturalism

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On the Internet, I have encountered a prominent Philosopher of Religion called Alvin Plantinga who was once described by Time Magazine as a America’s leading orthodoxist Protestant Philosopher of God. He has made many anti-naturalistic arguments and theistic arguments in the past, has engaged in Public Discourse with atheists, rather like William Lane Craig. And also, William Lane Craig seems to be a fan of Plantinga’s misguided “Reformed Epistemology”. But that’s another story altogether. In our particular case, I intend to refute the various fallacious absurdities of Alvin Plantinga’s “Evolutionary Argument Against [Metaphysical] Naturalism”. Or rather more specifically, I will be critiquing all six parts together of a six-part series of lectures on YouTube. It is a talk by Plantinga entitled “An Evolutionary Argument Against Naturalism”. —see here. I may not be able to address every point as meticulously as I would like to, but I will give it a fair shot. Of course, it is doubtful that he has not simply ignored these criticisms if they have already been made in the past. Oh well… also, for expediency, here is an overview of Plantinga from Wikipedia. You will notice that like William Lane Craig, he is a Christian apologist, and has authored such books as God and Other Minds, and has even written a book entirely dedicated to the argument he presents in this 60 minute lecture. 🙂

Continue reading Critique Of Alvin Plantinga’s Evolutionary Argument Against Naturalism →

Literature, Science

The Fabric of the Cosmos

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The Fabric of The Cosmos – Brian Greene

This book is a must read for anyone who is slightly apprehensive about reading books on complex physics due to it’s mathematical nature. Greene steers clear of any complex jargon, and explains ideas clearly an concisely, though you might find his use of characters from the Simpsons, and the X-files to explain relativity and quantum physics etc. somewhat patronizing (I certainly cringed a little bit at first, but I got used to it).

For example, he employs Lisa and Bart Simpson to explain Einstein’s theory of special relativity. He asks us to imagine Lisa shooting a laser off into the distance, and Bart chasing it on his high powered skateboard. The skateboard can travel 500 million miles per hour, whilst the laser travels at 670 million miles an hour. From Lisa’s stand point she would say that the beam of light was speeding away from Bart at 170 million miles an hour, however when Bart returns he states that the speed of the light was racing away from him at 670 million miles per hour. “If Lisa had been able to see Bart’s watch as he sped along at 500 million miles per hour, she would have seen that it was ticking about two-thirds as fast as her own,’ he writes. The conclusion is stunning: the faster you move through space, the slower you move through time – an amazing truth, but I think it could have been explained without having to invoke Bart and Lisa Simpson!

Greene takes you through classical Newtonian physics, to the strange and counter intuitive realms of relativity and quantum physics (subjects I’d previously found daunting, but was surprised to find that I could actually grasp the basics of it and even explain it to people after reading), before asking questions about the nature of time at the level of both the Einsteinian and the quantum, moving on the origin of the universe, string theory and M-theory, and finally the prospects of teleportation and time travel.

Though the chapters themselves are quite long, each chapter is divided up into several parts under subheadings, so it’s an easy book to pick up and put down again, without feeling too lost. There’s plenty of illustrations, to aid your understanding of some of the concepts that he explains (this is particularly helpful when it comes to the quantum physics).

All in all, I would highly recommend this book to someone who, like me who initially feels challenged by physics and cosmology. It’s a really clear and easy to understand book, and you will find yourself being thrilled by many of the strange and wonderful concepts that it takes you through. If you’re already well versed in physics and cosmology, you will probably find the explanations and analogies in this book too patronizing and laboured, but for someone who feels daunted by the subjects covered, it is a perfect book to give you a basic grasp of the laws that govern the universe we live in. The Fabric of The Cosmos is an inspiring and enlightening read.

Rating: 9/10

Review by: Laurens