Fuzzy Data

So let’s take a look at the Raelian PCR results that Jerry Coyne promoted as “science”:

Fig_1_Host_DNA

Here is how the Raelians explained it:

Negative controls (water as template, lanes NC) show no amplification product, indicating that PCR reagents were free from human or wheat DNA contamination. Human controls (lanes HC) show the expected 411 bp amplification product with human primers and no amplification with wheat primers, confirming that human DNA can be detected using the selected human primers. Wheat controls (lanes WC) show amplification products with both pairs of primers, with a more intense band with wheat primers. The human DNA detected in the wheat control was likely introduced during handling of the bread sample.

Here is Jerry Coyne echoing their explanation:

WC is the unconsecrated wafer control. As you see, it amplifies with both human and wheat primers (two bands on the “WC” lane in the left amplified with human primers), indicating the presence of some human DNA in the wheat control. This suggests, and it seems likely, that the purchased unconsecrated wafers were contaminated with human DNA when they were being handled. This happens sometimes: it doesn’t take much foreign DNA to show up as a strong band indicative of contamination; this happened to me when I was amplifying Drosophila DNA during an ancient sabbatical in Princeton, and got my own DNA instead).

Here is one reason this Raelian “research” would have never been published in a mainstream, peer-reviewed scientific journal (unless, I suppose, Coyne was the reviewer). The reviewer would have commented as follows:

Given that your wheat control was contaminated with human DNA, you need to repeat the experiment with a wheat control that is not contaminated. The WC is supposed to serve as the negative control, but because you contaminated it, it fails as a negative control. As the data stand, and because you have no negative control, it is not clear that you are working with a human-specific primer. Also, you need to indicate the base pair size of your markers (see here for how it is done). And you need to clarify whether Figure 1 is the only experiment you did or represents a typical result of x number of experiments.

Since Figure 1 is the only experimental result, and it is flawed, the paper would be rejected.
Furthermore, if the Raelians are trying to show the wafers have no human DNA, then how would they know if they had a positive result given that any positive result would be interpreted as human contamination? They need to devise a method to tease apart human contamination from a truly positive result.
Anyway, here is a even more serious problem with their data. When you look at the WC lane on the left side (doing PCR with human-specific primers), you’ll notice that there are 4 bands. There is the dark band on the top, a faint band below it and two more faint bands further down. Now, look at the HC (human control) lane – the three faint bands are not present. Human contamination can explain the large, dark band in the WC lane, but doesn’t explain the existence of the three faint bands in the WC lane. If those 3 bands are supposed to represent DNA from human contamination, why are they missing in the lane that amplified human DNA?
So what’s going on? One possibility is that the Raelian’s human-specific primer is not as human-specific as they think. Those three faint bands may represent something known as non-specific priming. Put simply, it may be that the human primers can weakly bind to spots on the wheat chromosomes and the three bands actually represent wheat DNA. That would explain why the three bands are not seen in the HC lane, where human DNA is being amplified.
But…..if this is the case, then why are those three bands missing from from lanes 1-4?

Okay, there are even more serious problems with what Jerry Coyne calls “science.”  We’ll look at that next.

Advertisements
This entry was posted in Jerry Coyne, Religion, Science and tagged , , . Bookmark the permalink.

4 Responses to Fuzzy Data

  1. J.P. says:

    What a waste of time and money.

  2. Rhaeyga says:

    Those are great questions and you obviously have more expertise in this area than I do, but I’d like to take a shot at them.

    This control is still useful, because it shows that wafers can be expected to be contaminated with human DNA. If transubstantiation was true (assuming the “substance” is DNA), then all consecrated samples should test negative when using wheat primers and positive when using human primers.

    According to the transubstantiation hypothesis (again, assuming the “substance” is actually DNA), no wheat DNA should be detected after consecration, and all consecrated samples should test positive using the human primers. Indeed, if all consecrated samples happened to show a 411 bp band using human primers, no clear conclusion could be drawn. But it did not happen.

    As to the last question, one possibility is that the human contamination in the wafer was prior to the baking. It is known that the process of baking bread breaks the DNA into small fragments (see Michael Tilley, 2004, Cereal Chem. 81(1):44–47). Some of those smaller fragments might have been partially amplified and recombined together through overlap extension, thus forming the 3 additional bands.

  3. Dhay says:

    That last paragraph aids understanding. Thank you.

    Something that I note is that (as Jerry Coyne himself points out) there was more human DNA in the unconsecrated control wafers than in the consecrated wafers (which had been additionally handled by both the priest and the recipient); and Coyne tells us some of the bars present in the unconsecrated wafers were not present in the consecrated wafers.

    This tells me — and should have told Coyne, who seems remarkably incurious about it — that the unconsecrated and consecrated wafers were not from the same batch, and possibly not even from the same manufacturer. The controls were not properly controls.

  4. Michael says:

    This control is still useful, because it shows that wafers can be expected to be contaminated with human DNA. If transubstantiation was true (assuming the “substance” is DNA), then all consecrated samples should test negative when using wheat primers and positive when using human primers.

    We don’t “expect” wafers to be contaminated because the control was contaminated. We note the control was contaminated and thus we have no true negative control. The solution is obvious – repeat the experiment with a non-contaminated control. For those who are not familiar with this type of lab work, it can all be done in a single afternoon with no additional cost (since they had the supplies). That these Raelians chose to post a result with a non-functioning negative control rather than simply redo the procedure speaks poorly of their work.

    According to the transubstantiation hypothesis (again, assuming the “substance” is actually DNA), no wheat DNA should be detected after consecration, and all consecrated samples should test positive using the human primers. Indeed, if all consecrated samples happened to show a 411 bp band using human primers, no clear conclusion could be drawn. But it did not happen.

    Is this similar to saying, “According to the evolutionary theory, if we mutate monkeys, they should transform into humans?

    As to the last question, one possibility is that the human contamination in the wafer was prior to the baking. It is known that the process of baking bread breaks the DNA into small fragments (see Michael Tilley, 2004, Cereal Chem. 81(1):44–47). Some of those smaller fragments might have been partially amplified and recombined together through overlap extension, thus forming the 3 additional bands.

    This is possible. But we have to assume pre-baking contamination not only for the WC, but also sample #5. Yet no pre-baking contamination for samples 1-4.
    There should be no need to guess/assume like this when the authors could simply repeat the procedure.

    I’m curious about something – why do you, like Coyne, have so much faith in a Raelian web-posting?

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s