A Baseline for LCN DNA Analysis

This came up in a discussion about JonBenét Ramsey. The main point in the discussion was that a baseline was needed for touch DNA analysis, which became synonymous with Low Copy Number (LCN) analysis. There is quite a bit of background here that needs to be covered as well, because this case will is also an example for this post. If you want to read the short answer, just scroll all the way down to the last line.

Background and Evidence

In 1996 she was found dead in the basement of her parents' home in Boulder, Colorado and the case is still unsolved. There has been much discussion of who actually committed the crime, some arguing the parents did it, others an intruder, but there is no resolution in sight. In a way it echoes the Azaria Chamberlain disappearance here in Australia in that there are people who think that Lindy Chamberlain killed her daughter and blamed the dingoes.

Back in 2008 the Washington Times reported that the Boulder DA had cleared the Ramseys (although Patsy Ramsey had died in 2006). Forensic Scientists had analysed touch DNA on the leggings that she was wearing on the night she died. This DNA matched DNA found on her panties.

Now it gets a little tricky here. DNA was also found under her fingernails the belonged to an unknown person. Now according to CBS News 48 Hours this DNA also matched that on her panties. I'm having trouble finding corroborating evidence for this, but assuming that it's all true we've got DNA from under her fingernails, DNA on her panties, and touch DNA from her leggings. Apparently these all match.

It's the last one that caused this discussion, but there is still a little more to cover.

What is "touch DNA"?

"Touch DNA" is a term that describes DNA that is left by touching an object.

The concept relates to Locard's exchange principle, which essentially explains the idea behind trace evidence. Whenever you do something you will leave a trace behind. It may not necessarily be DNA but it will be something from you. This includes hair samples, fibres, footprints and fingerprints. The opposite is also true, you will take something from the place you are at. This includes dirt in your shoes, other fibres or hairs and the like.

Touch DNA is an extension of this idea. Since some of the things that make up fingerprints includes skin cells it is possible to extract DNA from a fingerprint. However such DNA does not have to come from a fingerprint, it may come from other body parts as well, so your clothes will contain extractable and examinable DNA as well.

This article from the FBI analysed DNA gathered from clothing. They gathered DNA from both the inside and outside of the clothes and analysed it for DNA. Interestingly they found samples of DNA from other people including spouses and in one case from someone who nobody knew at all. The fact that this was from a newly opened package of hosiery made things all the more interesting.

This article was cited as evidence as to why a baseline was needed.

But before we look at that we will need to look at what LCN DNA analysis is.

What is LCN DNA Analysis? How does it relate in this case?

Low Copy Number Analysis, also called/considered a subset of Low Template Analysis, is the analysis of small amounts of DNA. Normally this analysis is used when regular Polymerase Chain Reaction (PCR) analysis doesn't provide a testable amount of DNA. The sample sizes that we are looking at here is less then 200 pg (about 2x10^-13kg). Normally samples contain about 0.5 to 2ng (5x10^-13kg to 2x10^-12kg) of DNA usually because you amplify it with PCR. The University of Leicester has a page on the subject.

PCR is best describes as a DNA photocopier. It uses the same proteins that are used in DNA copying, although the taq polymerase comes from Thermus Aquaticus, a thermophilic bacteria, so the polymerase is able to withstand higher temperatures, like those used to separate the DNA strands. It should be noted that it copies the DNA of everything that's in the sample, so contamination is a very real problem and great care is taken to prevent it.

Normal PCR amplification uses about 28 cycles. LCN adds an extra 6 cycles, so the amplification process uses 34 cycles.

As far as I'm aware there is, as yet, no data available as to how much touch DNA was gathered. It was assumed that it was a very small amount, so naturally it was assumed that LCN analysis was used.

Has LCN DNA Analysis been used in other cases?

In Australia such analysis was used in the murder of Peter Falconio. DNA was found on cable ties that were used to bind Joanne Lees. The DNA was found to belong to Bradley John Murdoch, who was later convicted of the murder. The court was told at the time that the odds of it belonging to someone else were 1 in 150 quadrillion.

In 2007 it was used in the Omagh bombing case in the UK. After concerns from the justice in the case the CPS suspended the use of LCN, and ordered a study. In 2008 the CPS announced that there was no inherent unreliability in the analysis.

It has also been used in cases like the murder of Anna Lindh, a Swedish politician, where the DNA came from a knife handle, and in the murder of Marion Crofts. This pdf from the Forensic Science Service has a few more examples.

So why a baseline?

The logic behind the baseline is that with the small amounts of DNA involved there might be an increase in the number of people falsely accused by DNA evidence.

Therefore a baseline of some sort should be found to see if the DNA is coincidental or not. The idea being once you have the baseline you will be able to discriminate between "coincidental" and "relevant" samples.

In my opinion though there is no way to statistically determine whether a sample is coincidental. The DNA needs to be processed and looked at in light of the other evidence. In the Ramsey case it's that this DNA appeared on the leggings, the panties, and under her fingernails. It was found to be the same DNA. But how did it get there?

DNA Transfer

LCN analysis is rather recent, the earliest case is from 1999, but the concept of DNA transfer is older, but has not been studied in great detail. There are plenty of articles out there though.

One of the issues brought up in the Ramsey discussion was that the DNA could have been transferred by JonBenét herself. Theoretically this is possible, but there is limited evidence that it did occur.

It depends on how it transferred, and also how much DNA was found. If we were to see transference we would see much DNA under her fingernails, and less on the clothing in the order that she put them on.

Now DNA transference can be ordered. Firstly we have primary transfer. This is DNA transferred when when you touch a doorknob, or a mouse, or shake hands with someone. The DNA is being transferred directly from you to the person or object. This is essentially a given.

Next is secondary transfer. This is when DNA is transferred to a third party. So let's say Person A shakes hands with Person B. Some of Person A's DNA will be transferred to Person B. This is primary transfer. Then Person B uses the same hand to open a door. Some of his DNA will be transferred (again primary), and some of Person A's DNA will be transferred. The latter is secondary transfer. Person A didn't touch the doorknob but some of his DNA is on it.

There have been studies that examine this. Lowe et al. examined this in the 2002 paper The propensity of individuals to deposit DNA and secondary transfer of low level DNA from individuals to inert surfaces (abstract here). They started by determining how good a DNA shedder the subjects were. Once they determined who was a good shedder and who was a poor shedder they washed the hands of the poor shedder and got them to shake hands with the good shedder. The poor shedder then touched an object and they used LCN analysis to see which profiles they found.

Turns out the poor shedder is a poor shedder for 6 hours after they wash their hands, and they managed to find the good shedder on the object.

However, Ladd et al. found in A systematic analysis of secondary DNA transfer (1999) (here) found no transfer, they also found that primary transfer was:

[H]ighly dependent upon the individual handling the objects or performing the handshaking.

Next is tertiary transfer. In the example with Person A and Person B tertiary transfer would be if Person C touched the same doorknob that Person B did. Some of Person B's DNA would be transferred to Person C's hand, and so would some of Person A's. The former is secondary transfer, while the latter is tertiary transfer.

I have not found any papers that deal with tertiary transfer. The closest that I could find was from G. N. Rutty in An investigation into the transference and survivability of human DNA following simulated manual strangulation with consideration of the problem of third party contamination (abstract) . The article doesn't examine tertiary transfer but uses it as a theoretical pathway as to how the unrelated DNA got on the "victim's" throat. Beyond that I've found nothing.

Parameters and Logic.

There are quite a few parameters that need to be examined. So beyond the level of DNA transfer, we would need to look at shedder type, so the odds of being a good/poor shedder, washing in general, how the people touch the object, and I think it would be fair to say the kind of object that they touch.

We are looking at a vast number of possibilities, and the reason for that is just to determine whether a sample is coincidental or not.

But we also have to look at the evidence. There is very little evidence for transfer beyond secondary. Anything above that appears to be theoretical.

But we must remember that logic would need to be applied based on the evidence.

So one possibility is that JonBenét came in contact with some guy's DNA. That somehow got under her fingernails. One suggestion for that is "dirty hands". She then touched her clothes with these fingers and the DNA transferred. So clothes wise we are looking at DNA that is at least secondary transfer DNA, but could actually be in levels that haven't been examined yet. The other thing is that when stuff gets under fingernails it usually stays there until removed.

The stranger possibility was that the DNA was on the panties when some guy at the factory touched them. I don't see that as logical at all, especially considering that the DNA under the fingernails was found and analysed far earlier then the leggings.

My own opinion is that it was a bunch of primary transfers. The DNA got under her fingernails by scratching, which is primary transfer. The DNA got on the leggings and the panties when the person touched them, which is more primary transfer.

But now I think it's time to answer the question.

Is a baseline even possible?

In my opinion it's simply no. LCN DNA already relies on standards set by the relevant government. It still needs to match 13 loci in the US. In the UK they would still need to match the 10 loci, and according to the University of Leicester the last 6 cycles are amplified in duplicate and alleles that appear in both can be used in a profile.

The legal standards will not change because the analysis is different.

One thing that I have noticed is that there are no baselines for other pieces of trace evidence. This is probably the most damning factor in the argument for a baseline. Why should one type of trace evidence have a baseline while all other types of trace evidence be exempt from such a baseline.

It's simply because there is no way to statistically discriminate between relevant and coincidental evidence. In a crime everything collected is potential evidence. It doesn't matter if it's touch DNA, a fibre, or blood spatter on a carpet, it's all evidence until it can be determined that it isn't. In a way it's backwards to what we would think. It's evidence until it isn't, not it's not evidence until it is.

Once we know that, say the vomit in the sink, actually belongs to a paramedic who didn't tell anyone that he threw up, it's potential evidence and should be processed accordingly. That's the reason why it's called an investigation. Because you investigate leads. There are no statistics that will allow you to discriminate evidence.

Lastly there is one other reason why a baseline is stupid. It's just one big red herring.

Lucifer

I was listening to a song (see the end of this post) and it got me thinking.

Lucifer, apart from being a saint which I just learned about, is commonly tied with Satan, the Devil, also known as the Prince of Darkness.

Although the latter does raise questions as who the King of Darkness the better question is why would you tie a name that means "Bringer of Light" with someone who people consider to be the "Prince of Darkness"?

Light is commonly used in Western culture at least (So I don't know about the use in other cultures, so sue me) as a representation of the "forces of good", and as a bringer of truth and also knowledge (The Enlightenment anyone?). So why the name "Lucifer" for a being that is supposed to spread lies and make us dumb?

I'm sorry but it's illogical, unless it's supposed to be the other way around.

Based on some modern day social controversies, such as evolution vs. creationism, or stem cell research, it appears that there are far more religious proponents on the side that would slow down, or even stop, humanity from learning new things, new enlightenments.

It does seem that religion wants to keep us in darkness, make us live in a world of superstition and monsters, to keep us down and hold us back.

Perhaps then the name is apt, for the enemy of someone who wants to keep us in darkness would be one that brings us light.

----------------
Now playing: Gregorian - Ave Satani (The Omen)
via FoxyTunes

Texas State Board of Education and Science Standards

Panda's Thumb reports that fifty scientific organisations have sent a message to the Texas State Board of Education telling them that their "Strengths and Weaknesses" passage is a load of rubbish.

But this isn't about the number of people/organisations who support an idea or set of standards (I'm looking at you, you list making IDiots), but instead what the overall message is.

In this case it's "don't teach your children crap because it's bad for Texas."

Anyway, at present the SBoE is voting on whether their "strengths and weaknesses" and other anti-science phrases is made part of their science standards, or as they will be known in the future "science" "standards".

The Houston Chronicle had liveblogged the discussion. Unfortunately for me I can only read about it becuase I don't know if I can find a copy of what was a live feed.

There was an opinion comment by McLeroy in the Austin American-Statesman (by the way McLeroy is the head of the SBoE) which has some very odd comments like this one:

The first step is to define science in a way that is satisfactory to both sides. Using new wording from the National Academy of Sciences, Texas' standards define science as "the use of evidence to construct testable explanations and predictions of natural phenomenon as well as the knowledge generated through this process."

This definition replaces the academy's 1999 language that was very controversial; it stated that science was "to provide plausible natural explanations for natural phenomena." The change from "natural explanations" to "testable explanations" is very significant. The old definition was inferior in that it undermined both the philosophy of the naturalist and the supernaturalist. By circular reasoning, the naturalist was prevented from using science to prove that "nature is all there is," and the supernaturalist was prevented from offering supernatural hypotheses. With the new definition, both the naturalist and the supernaturalist are free to make "testable" explanations. The debate can now shift from "Is it science?" to "Is it testable?"

I don't really see the point here. How exactly does the old phrase, with "natural explanations" mean that naturalists couldn't use science? I don't even see the supposed "circular reasoning" in the statement. It doesn't make any sense to me at all. His point on naturalists appears to be there just so he can try to give his point validity. The real point, as far as I can see, is his comment on supernaturalists offering supernatural hypotheses.

The thing is that in the end they haven't actually done anything, by his own admission the only reason why the changed it was to allow "supernaturalists", who are most likely the religious in this sense, to try and get their crap into science classes.

What I think makes it worse in this case is that he's gone and taken something from the National Academy of Sciences, which I believe is a very important body in the US regarding science, and has managed to utterly misunderstand the point they were making.

Those that believe in the supernatural won't be able to offer supernatural hypotheses using either definition of science. The latter because the supernatural is not testable, and therefore you can't actually construct testable hypotheses and in the case of the former because it is, by definition, not natural, so you could never use such hypotheses to "to provide plausible natural explanations for natural phenomena." See the use of the word "natural" there? No? Ok, nevermind...

The second statement was:

Once we have our observations, we can make a hypothesis. The controversial evolution hypothesis is that all life is descended from a common ancestor by unguided natural processes. How well does this hypothesis explain the data? A new curriculum standard asks Texas students to look into this question. It states: "The student is expected to analyze and evaluate the sufficiency or insufficiency of common ancestry to explain the sudden appearance, stasis, and sequential nature of groups in the fossil record." It should not raise any objections from those who say evolution has no weaknesses; they claim it is unquestionably true.

So. Much. Wrongness.

For those playing at home you should know that evolution is only semi-random. Yes, all the stuff involving genes is essentially random. However evolution is not just genotypes and phenotypes. Using his hypothesis you see the flaw about "unguided natural processes". Usually when creationists say "unguided" they really mean "random". It's just that "unguided" sounds more scientific, it's the same choice of words that quack doctors use to convince the scientifically illiterate that their stuff is genuine.

If someone can care to show me that "unguided" is not used by creationists as a synonym for "random" please do so.

What he is ignoring are things like sexual selection, predation and environmental factors. All of which are non-random, and affect evolution.

Lastly, he isn't actually referring to evolution at all, but common descent.

And the way that they suggest that students learn about common descent? Something completely stupid.

"Here is a bunch of fossils. See how they don't show conclusively that everything is descended from one thing? Good. Now you see how evolution is wrong. No Bobby, don't look at that evidence over there that proves that it's right. No, we're only allowed to use the fossil record."

Frankly I couldn't care less about "weaknesses". As far as I can tell the real possible "weaknesses" are actually at a level that is far beyond the level that the students should be at. The reason people complain is because what is being suggested is so blatantly wrong. It's making children learn that something is wrong by only looking at a small subset of the evidence.

I don't really have too much to say about the meeting at present. The liveblog, which I linked to above, covers it really nicely.

Wild Dolphins Tail Walking

I know it's not a very creative title, but I'm just nicking the title from the BBC.

You would expect that something interesting in the realm of science would appear in, I don't know, The Advertiser but it hasn't.

From what I can gather, Billie picked up the trick when she was taken to a dolphinarium when she was injured and she taught the other dolphins in the Port to do this trick.

I had better explain that sentence a little better.

Port Adelaide is home to the Port River Dolphins. This pod lives in the Port River and along the Barker inlet. These dolphins are the only wild dolphins that live within a city.

Naturally they are also something of a tourist attraction. I guess people can sort of ignore the rather ugly Port when they are looking at dolphins.

Anyway, the scientists don't seem to have a clue as yet as to why they are tail walking. I know that they wouldn't be getting food out of it from the tourists because you can't feed them. I suspect that the boats might have a little to do with it though, maybe helping to stir up fish or something so maybe they are trying to get more people out there so they can eat more.

I personally have no idea.

Billie, the dolphin mentioned in the story is a wild one, as all of the dolphins in the Port are. She is also one of the first dolphins to have been found there.

Either way, if you are ever in Adelaide, you should make the attempt to see the Port River Dolphins. There are also quite a few museums in the area that you can look at as well.

Solar Eclipse

Once again from the BBC, the Northern Hemisphere saw a total solar eclipse, or at least if you were in the right spots of Russia and China, and maybe Canada.

I've seen a total solar eclipse, and it is breathtaking.

I saw it back in 2004 when one crossed over South Australia. People were flocking to Ceduna, which was one of the few towns along the line where the eclipse looked its best.

However, my family and a few friends didn't go to Ceduna, which would have been packed.

We were up north. Just outside of Woomera, in the Restricted Area. One of our friends knew the owner of Wirraminna Station so we could enter the Restricted Area without any problems.

On a side note, if you have ever been to the Outback, you will know that it is a very beautiful, but deadly, place (and in our case, packed with flies, stupid annoying flies.)

We arrived a few days before the eclipse and saw some of the things that you could see and also set up our tents.

The day of the eclipse the small section of the Stuart Highway that was set up for people to view the eclipse was packed with people (we drove up to see).

We however saw the eclipse in our campsite, a secluded, wooded place in the middle of the desert. The red sands covering the ground. The small, stunted trees around us. There was nothing for miles.

The moon started it's transit over the sun, and when it reached totality everything was quiet. You could hear a pin drop. The Outback was covered in an odd blue hue (I remember clearly, that it was not black) and for such a short amount of time everything that mattered on Earth was meaningless.

As the moon moved away from the sun it was like a strange dawn over the desert.

And we all went back on with our lives.

Answers in Genesis Has A Journal?

I saw this on Panda's Thumb.

Answers in Genesis have their own "peer reviewed" "journal".

I must admit though that their page with the articles in it looks nice, and at least it's free for people to make fun of.

This one caught my eye.

Entitled Microbes and the Days of Creation without proper stupid protection you will lose several IQ points.

The abstract alone makes me think immediately of this (as a side note, the owner of that site is apparently on Myspace, and although wrong at times isn't really that stupid).

Clearly though they are trying to reconcile the lack of microbes with a literalist interpretation of Genesis.

The argument is as follows.

It's simply that micro-organisms exist in symbiosis with plants and animals. So nitrogen fixing bacteria that are found with peanut plants for example were created on the third day, with the rest of the plants etc. etc.

We do get to an interesting position though.

You know how some people believe that humans were created in the image of God?

Well then either God is actually a giant E. coli bacterium, and that humans were created to house that which was made in his image, or E. coli are just as important to God as we are. I mean the neutral E. coli are quite useful to the body.

If God was supposed to have made his creations perfect to begin with, why have a bacterium in you that gives you Vitamin K₂ but can also give you food poisoning if you have a specific strain?

Then there is the section on viruses.

It reads like the "good" viruses are there to help humans, when in fact they would be doing what they are doing to "survive". What exactly would you say for the undead or non-live?

For pathogens and "bad" viruses, well they are easily explained by the standard creation argument. Yep that's right. The "fall" was responsible.

I guess back in Eden HIV went about making people happy and immortal or something stupid like that.

For some reason I feel as if what I read is completely useless for science.

Wait a minute, no I don't.

It is completely useless for science.

Like everything in creationism there is no use for this "paper". It doesn't explain anything for science, it explains how creationists think, but not science.

Unless this AiG "peer reviewed journal" is actually an elaborate humour site it's rather pathetic to see them having to make their own journal, I guess they thought that proper journals wouldn't publish their stuff.

It's a creationist version of the Journal of 9/11 Studies.

ITK Blocker a Cure For AIDS?

Well no actually, but it is a catchy title.

According to the BBC, Proceedings of the National Academy of Sciences (A pdf can be found here) reported that it has been found that blocking the ITK protein causes a decrease in HIV replication. Here is a better page from MedPage Today.

In really simple terms what they have found is that blocking ITK can slow down the progression of the virus in quite a few ways:

1. Impedes infection
   
2. Slows down replication

Clearly it doesn't stop HIV from being transmitted but it sure screws things up for the virus.

If you want a Numb3rs-type analogy I would say think of your own but make sure that it has zombies in it.

Apparently the effect that it has on us is just a slowed immune response, but we are not completely harmless.

But it does show a change in the way we are thinking of combating HIV. Instead of trying to kill the virus itself, which mutates quickly and is slowly becoming immune to the drugs, we are looking for ways to make our own bodies a rather hard place for it to survive. Such a drug that could block ITK production in T cells would mean that instead of developing drugs to combat viral infections we develop drugs that make it harder for viruses to infect you in the first place.

Think of the benefits, although we do need more testing to see how adverse the side effects could be.

Ape Fossil Found

Physorg had a report on an ape fossil that might change the idea of how we evolved forever.

It's about 10 million years old, which is near the time where our last common ancestor with the great apes (although this fossil is about 2 million years older then the current point in time when we diverged though).

Annoyingly the article was titled: "Rare great ape fossil challenges evolutionary theory: study" which means that it will probably be quote mined (ugh, right now I'm getting myself dirty by looking on uncommon descent to see... unclean, unclean, it's not coming off...), and used as an example of the supposed "imminent demise of evolutionism".

I can't think of any ways that they might quote mine the article, but I guess when I can find the paper and read it myself I might find something in there for them to quote mine.

It isn't though.

It seems that what they have found might contradict an idea that involves apes migrating from Africa to Europe and Asia, the African population dying out or something like that, and then evolved forms of the European and Asian populations returning to Africa.

All that we see here is science being scientific. An existing idea that was supported by the evidence may now become obsolete and a new idea will take it's place. It is this method of finding ways to explain the world based on the evidence is what separates scientists from creationists (and also a certain 9/11 CT that I have been arguing with).

We may also see in the future more fossils of as yet unknown ancestors to the great apes being found.



----------------
Now playing: Beck - Nausea
via FoxyTunes

Peppered Moths

One of the finest examples of evolution is the Peppered Moth or Biston betularia. In fact it is so great that I am learning about it again in first year Biology. This is also the first post that I have written discussing Creationism so I hope I don't stuff this up.

Now I don't know if I can really say that I love Biology, I must admit that I prefer Chemistry but for me to live up my dream I need to understand something about Biology anyway.

Now for those that don't know the Peppered Moth (I prefer the common name, less italics to write in) can be found in the UK and can be found in two varieties a melanic variety (which is dark) and a lighter form.

Although the experiment undertaken by Bernard Kettlewell in the 1950's the effect started from the beginnings of the Industrial Revolution.

Before the huge increase in factories the forests were clean and had light coloured lichen growing on the trees.

The lichen allowed the lighter moths to survive easier compared to the melanic ones because they could easily camouflage themselves on the trees and not get eaten by the birds that preyed on the insects.

Naturally the darker moths were easier targets and were eaten.

However the Industrial Revolution changed the rules.

The drastic increase of factories spewing out smoke created plenty of soot that killed off the lichen and covered the trees in black soot.

The colours of the moths changed. The melanic moths started to become more common, not being the rare variety anymore but the common one.

Kettlewell managed to show in his experiment that the darker moths were prevalent because the birds found it harder to find them in the soot covered forests.

After the 50's with a program that cut down pollution they found that the moths returned to their original colour diversity.

Now creationists seem to have a problem with this trying to find ways of disproving the hypothesis. The Panda's Thumb mentions them claiming that the results were "faked" and Talk Design has an article that quite thoroughly shows how first the creationists are wrong and how the book Of Moths and Men is also wrong.

This site which is probably getting more exposure then it should, says the following:

IMHO...a couple of issues with the most recent peppered moth study. It's still a moth, and the evolution is an oscillation of populations, just like the finches of Galapagos. Of course, the Darwinists will appeal to the "great creators", random chance, natural selection, and the jackpot, hundreds of millions of years. Given enough time, anything can happen, right?

What we see here is what we can call 'a quite stupid comment'.

It isn't the worst that I have heard from a creationist. The number one thing is a tie between someone claiming that macroevolution was "a rock turning into a banana" or "the Peppered Moth isn't an example of evolution because the pollution was man made but evolution is natural"

Trying to claim that the Peppered Moths has nothing on evolution because it is "still a moth" is a moot point. What was shown here was that the moths adapted to survive, those that were born melanic in a dark environment meant that they were more likely to survive.

The evolution was not just an "oscillation of populations" it was an increase/decrease clearly in the allele frequency of the population. Which, anyway, has nothing in common with the Galapagos finches. The Galapagos finches arrived on the island, most likely from a storm on the mainland and over time they reproduced but they also filled unfilled niches in the ecosystem. The one that I can think of at the moment is the Warbler Finch which is a finch that has adapted itself into a type of warbler, but it is still a finch.

The next line of that comment is just standard creationist drivel, make it sound like a religion and somehow it becomes an idea that is characterised by a belief system but clearly shows a lack of understanding of evolution.

Random chance only affects life if it is something that does not target specific species, for example an asteroid hitting the Earth. It doesn't discriminate between a fit animal and an unfit animal it just kills and whatever manages to survive is bloody lucky.

What he calls the "jackpot" (millions of years") is not always the case. It does not take millions of years for bacteria to become resistant to types of medicine, nor does it take millions of years for various species to become immune to the effects of bacteria like Wolbachia.

To finish, what makes creationists funny (or even IDers) is that they try so hard to disprove something but they don't understand the thing they are trying to disprove, so they fall back to fallacies...

Yes it is. Here is the complaint to prove it.

This is the more informative part of the PZ Myer "lawsuit", the one where I have read the things that I should have read last time but needed sleep.

Now reading some comments I heard that some real media sources said something about this. Too bad us bloggers have decided to talk about it.

The closest that I seem to have found is that the blog for Scientific American has said something.

Now nicking this link from PT takes us to the complaint in question.

I might as well point out now that the plaintiff is Stuart Pivar. The guy who wrote the book Lifecode. It is the review that has caused all the problems.

Reading the complaint I see many facts that seem to be completely pointless to me, I would say that paragraph 10 in the complaint (3^rd fact point) could really be some sort of appeal to authority.

Paragraph 10 states:

In 1982, with the late, celebrated artist, Andy Warhol, Plaintiff co-founded and provided the initial funding for the New York Academy of Art, a classical graduate school for painting and sculpture, whose current patron is H.R.H. Charles, Prince of Wales

As I said, what is the relevance for this?

But back to the point.

Here is the review by PZ Myers (Which is a repost). Here is another comment posted on the same day.

The biggest problem is that they don't mention in the complaint which post they are complaining about, the review, or the reasoning behind reposting the review. I suspect that it is the latter because the facts seem to fit it.

Paragraph 15 is the really the start of the matter at hand.

Paragraph 15 states:

On July 12, 2007, Defendant Myers launched a vicious attack on the integrity of Plaintiff's work on Myers' "Pharyngula" webiste, found on the internet at www.pharyngula.com.

(The hyperlink has been added in by me and is to the correct address).

Now then, from what I can see the post in question has no attack whatsoever, and can hardly be called vicious. The closest thing that I can even see as an attack is the use of the tag 'kooks' but bloggers everywhere should know that tags are completely opinionated. I could write a post about someone and use the tag 'wanker' if I wanted to (not that I ever will or may the almighty Google delete my blog), but it has no bearing on the actual person. But that is probably a false analogy.

What PZ Myers seems to have said is that the whole premise of the book is flawed.

The second post is just his annoyance about the media giving a book that has an idea that he thinks is completely pointless any time whatsoever. I see no attack just some criticism.

Paragraph 16 states:

On July 12, 2007, Defendant Myers maliciously, and without cause, defamed Plaintiff by referring him to as "a classic crackpot"

Last I checked in countries with freedom of speech that is not a crime. There are far worse words that you can use to insult someone. Does that mean that a psychic will sue James Randi for calling their stuff "woo-woo"? Or homoeopaths suing because he claims that their 'medicine' is a hoax?

Paragraph 17 states:

Upon information and belief, Defendant Myers' references to Plaintiff as "a classic crackpot" were necessarily intended to disparage Plaintiff's abilities as a scientific enquirer and were intended to hold Plaintiff up to ridicule and embarrassment in this specific area of Plaintiff's professional endeavors.

PZ disagreed with the argument, he is allowed to do that.

Paragraph 18 continues with the supposed defamatory remarks somehow coming up with the conclusion that Myers somehow holds complete sway over the entire scientific community and that by calling Pivar a "crackpot" means that his endorsements will somehow go away.

Paragraph 20 made me laugh:

Because Defendant Myers' defamation of Plaintiff has been disseminated widely throughout the world, his remarks were also likely and possibly intended to hold the Plaintiff up to ridicule in his business relationships as an industrialist, Plaintiff's social relationships and in his activities as a philanthropist

Now Pivar is the founder of Chem-tainer Industries (paragraph 9) , a business that has absolutely nothing to do with matters of biological research. I honestly doubt that people would stop business with his company because he has ideas that have been called 'crackpot'. It doesn't stop the other crackpots now doesn't it?

The same goes for Philanthropy. I am sure that nobody there would care that he has published a book that has been labelled as 'crackpot', it isn't as if he had committed mass murder or something like that.

The biggest irony is that he is really shot himself in the foot here. People would have read the entry by Myers, thought little of it, perhaps even bought the book so they could read for themselves what this guy was going on about and that would have been it. Now pretty much the entire blogosphere is talking about it, he is now being ridiculed because he decided to embark on a frivolous lawsuit.

Paragraph 21 cites the case McFaddn v United States Fidelity and Guarantee Company as possible precedent claiming that "crackpot" can be a slanderous term. Looking around (and managing to find something from Richard Dawkins) it looks like the case never went further then the Mississippi Court of Appeals, which means that they are citing non-binding precedent because I assume, as it is done here, only federal courts can produce binding precedent.

Paragraph 22 says that Myers has just decided to keep on attacking the book.

Paragraph 23 says:

Upon information and belief, [Neil de Grasse Tyson] has withdrawn any previous review of Plaintiff's work in relation to Lifecode due to the unwarranted and vitriolic attacks Defendant Myers has made on Lifecode and Plaintiff personally.

However they do not say what information Tyson received or why he wanted his comments removed. I managed to find them on Butterflies and Wheels, which found that the quotes were either taken out of context and made up.

Pivar had a few people to support the book, Richard Milner, Robert Hazen, Brian Goodwin, Dimitar Sasselov and Neil de Grasse Taylor. Taylor decided to have his comments taken off the website because they were false and it seems that Pivar has somehow attributed lying on his part into "PZ Myers convinced him through ad hominems". PZ Myers himself stated that he received a copy of the book to review ("Instead, Pivar sent me a copy of his book to review, so I'll focus on that.").

Also notice that if you look at the reviews section the one from Hazen is the longest on that page but he admits that he is not an expert in "this area of topology and mechanics" he says many things that make little sense to me but all the reviews no matter how long are supportive of the claims so what is wrong with a dissenting view.

Because of his standing in the blog community (He is considered the best of the science blogs) I suspect that Pivar would have thought that it would have been good to get a positive review from him, but it backfired when the brutally honest review (paragraph 19 says that Myers has described himself as a cruel and insensitive person), was a negative one.

So Pivar writes another version of Lifecode called Lifecode:From egg to embryo by self-organization which received an "even worse" comment. This would have annoyed him so he ends up with the decision to sue PZ Myers, which really is shooting himself in the foot.

He didn't get the result that he wanted and is now trying to get his revenge.

Paragraphs 24 - 27 are there to try and argue why the parent company is at fault.

Paragraph 28 says that Pivar mentions (on July 17 2007) that Myers had reviewed the earlier book.

All I can say is the Myers seems to have been getting messages from Pivar well before the second review came out.

This is the link to the second review, which is another negative one.

Paragraph 30 states:

Defendant Myers' defamatory remarks have caused the Plaintiff considerable mental and emotional distress

From a guy who has been bullied in the past let me tell you something. A bad review is nothing. If I could choose between getting a bad review or having a mob of people yelling names at me I would choose the review.

Paragraph 31 is trying to say that Myers has ruined the work of Pivar as a scientist, who I guess is most likely more at home in a Chemistry lab then a Biological one.

Paragraph 32 states:

By reason of the defamatory comments written by Defendant Myers and published by SMG, Plaintiff has been damaged by loss of book sales and diminished return of ten years of funded scientific research in special damages, a sum in excess of [US]$5 million.

(I added the [US])

Now from what I understand the suit is for US$15 million. So I guess the breakdown is US$5 million for supposed people not buying the book, and him not getting money for research. Even according to Amazon.com's "About the Author section, Pivar has no credentials in Biology. It says Physics, Mathematics, Chemical and Mechanical engineering.

In all honesty I doubt that he would get research grants for Biological work.

The final paragraph of fact, 33, claims that he has:

[Suffered], inter alia, the special damages referenced in Paragraph 30 supra, and gross impairment of his good name, public embarrassment, humiliation, impairment to his professional reputation, public impairment of his abilities and integrity, anxiety, emotional upset and public ridicule.

Well the public ridicule of him would really have increased since he decided to slap a lawsuit on PZ Myers and SMG and the other things are just complete rubbish from a guy who is trying to garner sympathy or is someone who can't handle criticism.

The declaratory relief says that he wants Myers to remove anything negative written about Pivar from his blog. What an interesting way to silence critics. If that happens then I will willingly give space on my blog for PZ Myers to post whatever the hell he wants and I am sure that others would be willing to do so as well.

The second claim is about business interference and the US$5 million.

The third claim is where the rest of the money appears, the US$10 million. That is damages for libel per se.

The next section is where it gets scary. Under 'Prayer for Relief' comes the reasons what Pivar wants to get out of this. I will copy this herein:

PRAYER FOR RELIEF
WHEREFORE Plaintiff respectfully demands this court enter judgement in its favor and against Defendants Myers and SMG as follows:

1. Enjoining permanently the Defendants from making any future defamatory statements about the Plaintiff and immediately removing any remaining defamatory statements from their websites

2. Awarding on the Second Claim for such compensatory and punitive damages for the Defendants tortious interference with Plaintiff's business relationships as a jury may impost, but at least the sum of [US]$5 million, that constitutes Plaintiff's special damages.

3. Awarding on the Third Claim, such compensatory and punitive damages, inter alia for emotional distress and loss of reputation of at least [US]$10 million, or any sum as the jury may impost.

4. Granting such other and further relief as the Court seems just and proper, including the costs of this action.

What makes the whole thing scary is that would silence Myers from posting anything on his blog that criticises Pivar. Which may leave Pivar open to write a whole bunch of crap and pass it off as science.

It also would open the door up to other lawsuits against other people who criticise someone, even in book reviews where the book was sent to the reviewer by the author personally. It would also turn the US blogosphere upside down because they cannot say things that criticise.

Blogs are primarily an opinonative thing, we are not the proper media, we write about things we want to write about, we are not the news where we must be completely neutral on all issues, what makes a blog great, like Pharyngula or PT, Baghdad Burning or the BABlog. We know that they have a bias, but that is what makes them good to read, they have viewpoints that they support or don't support because they are written by real people, from real places in the world, about issues and situations that are important to them.

Do you really want to see that disappear in a blink of an eye?

Frivilous?

I found this on The Panda's Thumb.

It isn't really nice to hear.

At this point in time it is rather late here so I won't say too much at the moment in regards to facts, my opinions however can and most likely will make me late for my Marine Science lecture tomorrow.

PZ Myers, the excellent author of scienceblogs.com/pharyngula/>Pharyngula has come under attack because he decided to be honest when he wrote a review on a book written by some creationist.

So now he and Seed magazine are under attack by this guy who is claiming, supposedly that PZ Myers (Who has nothing to say on the matter) used the review to ridicule the guy who wrote the book that he was reviewing.

So what?

If I write a really bad book should I honestly expect that the reviewer to be really nice and not hurt my feelings?

If I do then I am thinking like a complete idiot.

Now here in Australia we all know that we have some rights, although technically not enshrined anywhere (the Constitution lists two fully if I remember correctly and touches on a third one) but we know that there is a point where you can't do a thing when it comes to words.

There are some problems, like a fencing company having to take down a sign for a supposed rude word even though it is a rather clever play on the word 'erection'. If you have thought of anything except building fences, then, shame on you.

In the US from what I hear there seems to be a very weird way of doing things. It seems that you have a right to say whatever the hell you want, but you can't insult someone?

I love how there are blatant contradictions of freedoms like this.

I don't know what was written because I haven't looked yet, but I do know that as long as PZ was within the law, and I feel confident in saying from what I have read of his blog, he has, he can say whatever he wants.

If he gave the book a poor review then he gave it a poor review.

No need to sue someone over it.

Or supposedly claim "considerable mental and emotional distress" and demand financial damages.

Having your name run into the ground by the media for something you didn't do, that causes "considerable mental and emotional distress, getting a bad review doesn't. Most authors get bad reviews once in a while, they don't sue people over it.

It's like asking for US$15 million for financial compensation...


...

oh, yeah that is the amount he is being sued for...

...

Now US$15 million is a ridiculous amount to ask for after being given one bad review. It's quite like asking for $7 million because your $2 clothes peg broke. The amount wouldn't even fit a proper slander crime in this case.


There is one good thing though. If the media start going on about it there would be a lot of free publicity for PZ Myers, and they say that any publicity is good publicity.

Unless you happen to be that US Gridiron player who pleaded guilty to the dog fighting ring...

The Ancient Ones Return

Reading through the BBC I found two articles that interested me.

The first was the discovery of an ancient forest in Hungary.

The trees, identified as a species of Swamp Cypress have been buried for about 8 million years, and protected by a layer of sand which kept the 16 specimens safe while the rest of the forest was buried.

Now there is something of a frantic rush to save these trees, because they are now unprotected and at the mercy of the elements, but I personally feel confident that they will be safe. However the productivity of the mine will collapse because they have found that they can't move the trees failed.

Really they are just tree trunks, about 6m high and 2-3m wide.

However the insight that they can bring. They can give a good idea as to the climate of the region for around 300 years, 8 million years ago.

And the next item that I have found takes us to a lab.

Scientists have managed to 'restart' some ancient microbes

Well, maybe 'restart' is not the right word, perhaps 'reawaken', but anyway the story.

This happened about a week ago though but it is still interesting.

What they have managed to do is revive various strains of bacteria that lived from around 100 000 years to 8 million years (I wonder if they knew the trees? Probably not because they are in Antarctica...) ago.

The results are interesting.

They have found that the oldest microbes reproduced slowly compared to the younger ones (doubling about every 30-70 days instead of about a week). They suspect that they have been damaged by radiation because they have also had trouble finding out what the oldest stuff was.

They found that the DNA will degrade exponentially after 1.1 million years, so the chances of finding a microbe with a full undamaged genome is highly unlikely, but the possibility is still out there.

This is probably some decent evidence pointing away from life having arrived on Earth from something else, but we never know.

The younger microbes are very interesting though.

DNA testing found that there were examples of common bacteria among them. They found forms of protobacteria, this phylum is home to commonly known pathogens like E. Coli, or Salmonella. The firmicutes found are part of the same phylum as Staphylococcus, or, if you work in the hospitality industry, Listeria. A final example in the news article was the actinobacteria, which have modern relatives like the Micrococci, including the bacteria well loved by deodorant companies Micrococcus luteus which helps to cause the bad odour when you sweat, or another bacteria loved by other companies Propionibacterium acnes which causes, well you can guess the well known condition that usually affects people in their teens or people the day they have a hot date...

Anyway.

What makes these young microbes interesting is that DNA testing also found few matches, which indicates that the DNA has genes currently unknown to Science. So they may not have been isolated yet or we have not found a modern example of the genes that we don't know anything about.

What would these unknown genes do? Are they just simple ones that regulate processes or the creation of certain proteins? Or are they genes that could have a more sinister purpose? Or are they genes that could provide cures for diseases?

Now interestingly a few days before this came out NASA launched their probe to Mars (The Bad Astronomer has a pretty good picture of it on his blog) which is going to look at the ice caps of Mars, and take some samples to be analysed on Earth.

Wouldn't it be interesting if they found some cells there with DNA similar to the ones found here?

I doubt it, but they would probably find better examples of the genome of whatever appears on Mars. Perhaps any examples of life might have developed a different way of storing information?

Update: I spoke to the Bio lecturer today who had experience with things like this and he said that in regards to the trees they can probably cover them in something that would protect them.