What are the odds?

Another “soft tissue preservation” article from Brian Thomas today: “Scientists Broom Challenging Discoveries Beneath ‘Contamination’ Rug.” He means “sweep” there instead of “broom,” which I don’t think it supposed to be a verb. Thomas hasn’t got a new find since last week’s, but instead does a more general overview of the concept:

Recent years have witnessed many revolutionary discoveries of original tissues in fossils. Each new find challenges the widely held notion that fossils formed millions of years ago. After all, lab tests repeatedly show proteins and other biological materials lasting no longer than hundreds of thousands of years—millions are out of the question. As a result, these fossils clearly look like recent deposits. What tactics do evolutionists use to accommodate these original organic remains into their entrenched belief in deep time?

The claim that “lab tests repeatedly show proteins and other biological materials lasting no longer than hundreds of thousands of years” is one of the great ironies of young Earth creationism: as Ken Ham would say, “were you there?” In this case there really are reasons to doubt the results of laboratory experiments on this subject. In October we looked at a study that calculated the half-life of DNA from Moa bones, giving a figure of 521 years at room temperature. The data and conclusion of this study could be fitted into the YEC timeline so, naturally, Thomas accepted it and used it to attack more ancient claims. What I found most interesting, however, was when the paper said that their real-world result was nearly 400 times greater than the conclusions of lab experiments. Those “lab tests” really aren’t reliable, and so if you use soft tissues to try to calculate the age of a fossil and it conflicts significantly with a radiometric date for the same find then you would be best to discard tissue number in favour of the radiometric one on the grounds that the latter is going to be much more reliable than the former.

Getting back to Thomas’ article today, he says:

One tactic is to simply turn a blind eye to the whole fossil tissue issue. A possible example of this occurred when an ICR employee attended a 2010 debate featuring the late atheist and evolutionist Christopher Hitchens. After the event, the employee asked Hitchens what he thought of blood vessels recently found in Tyrannosaurus rex bone? Hitchens replied that he knew nothing about it.

The article gives no more details about the event than to cite the story to Schweitzer’s 2005 Science paper, Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex – hardly hot off the press at the time. Thomas goes on:

His ignorance conveniently insulated him from having to reconcile data that refuted his secular view of history. How could such a prominent author on origins topics have for so long “missed” all hints of paleontology’s most game-changing discoveries? Shouldn’t an expert be well read in the very subjects he debates?

This tactic seems to be a modified Gish Gallop. The normal strategy of that name involves making so many different arguments that it’s impossible to refute them all in the time available, leaving the opponent looking like they don’t know what they’re talking about. This case, however, involves asking the opponent about a specific topic and tut-tutting when they’ve never heard of “paleontology’s most game-changing discoveries.” I didn’t know that Hitchen’s was a palaeontologist (or even that he wrote about that kind of “origins topic”), or that we should take the word of creationists on what makes important scientific discoveries. Even from the other side of the world we are hearing a lot these days about the cottage industry of US Republicans effectively making up scandals and claiming that they’re “bigger than Watergate” – this seems to me to be quite similar.

Some deny the science showing that the tissues are real proteins, and others deny the science of tissue decay rates. Biblical creationists deny the millions of years—rather than the science—and this actually solves the key dilemma.

Denying the millions of years simply creates more problems – how do you explain the radiometric dates, and why don’t all fossils contain large amounts of tissues if they’re all young? – while the other options (especially calling them contamination) don’t.

But secularists who do at least look at the soft tissue fossil reports deploy another tactic. In response to the recent discovery of original protein inside tiny dinosaur bones from China, Smithsonian Institution paleontologist Hans-Deiter Sues cited contamination. Supposedly, the proteins in question recently “snuck into the fossils” from some source other than the fossilized animal.

He told Science NOW, “You can never really totally rule out contamination.”

This is the egg find we looked at last week. “Snuck into the fossils” does not appear to be an actual quote, and Thomas’ derision for the idea is entirely unjustified: contamination, which can occur in many ways, is a real concern.

Technically, his statement is scientifically accurate. But it can lead to absurd conclusions. If one can never totally rule out contamination, then one can always excuse the data by claiming it—playing the convenient “contamination card”—even when it defies common sense.

For example, one can never totally rule out the possibility that my plate of dinner is contaminated. Instead if it coming from my kitchen, another person might have cooked the identical meal elsewhere, then secretly set the full plate of food on my table. Though possible, this contamination speculation is so unlikely that it can be ruled out on the basis of its extreme implausibility.

This is quite a stretched analogy. Closer to the reality here would be if you tested the protein contents of the cooked food, and found low levels of intact protein as if it had never been cooked. You would have two choices here: you could conclude, against all other evidence, that it was never actually cooked; or you could conclude that the protein came from some contaminant, such as the raw salad on the other side of the plate or from the bacteria that have settled on the food since it was cooked.

What quality of soft tissue fossil data would similarly refute claims of contamination beyond reasonable doubt?

How’s this: a recent study extracted ~10,000 year old DNA from the sea floor. They’re pretty confident that they’ve ruled out contamination, saying:

Other ancient DNA studies have been discredited after supposedly ancient genetic material turned out to be modern contaminants, but those fears don’t apply to this new research, says micropaleontologist Michal Kucera of the University of Bremen in Germany. He says that both teams took the necessary steps to avoid contamination, and their results don’t look like contaminants. In the Biology Letters results, for instance, DNA from older sediments is more degraded than material from more recent sediment—not what you’d expect if the DNA were a laboratory stowaway.

The ~10,000 year date is recent enough not to fall afoul of any reasonable “that’s impossible!” challenge (too old for the YECs still), but that doesn’t mean that they don’t have to worry about contamination. Scientists will still raise that as a possibility even if there’s no need to “sweep it under the rug” – there’s no conspiracy. This study does look like they’ve thought of all possibilities, however. Whether you could be similarly certain of something much older I don’t know.

Now, Thomas has a chart for us. He says:

This chart contrasts the maximum time required to convert bone collagen into dust with ages that the secularists themselves assigned to collagen-containing fossils. The tiny red column represents the maximum age of bone collagen determined by repeated decay measurements. It assumes that unrealistically cold temperatures preserved collagen for as long as one million years.

So he’s basically saying that collagen can only last a million years, and he has seven examples of much older finds. Here’s his list (hotlinked & claimed as fair use):

Thomas' graph

The first two entires – the T. rex and Hadrosaur – would appear to be Schweitzer’s stuff, which I don’t feel that I can conclude whether they are or aren’t the result of contamination. Here’s one occasion that her research has been mentioned on this blog; there are many others.

Back in late July of 2011 I investigated a list written by Thomas of soft tissue finds. The result was this page, which I don’t really recommend that you peruse as it’s poorly spell-checked and the navigational system (which involved links placed on a copy of said list) no-longer works properly. However, it does provide information on the next four items above. First, the mosasaur:

31. Convergent Evolution in Aquatic Tetrapods: Insights from an Exceptional Fossil Mosasaur:

Authors: Johan Lindgren, Michael W. Caldwell, Takuya Konishi, Luis M. Chiappe
Link: full text
ICR Description: Mosasaur blood, retina
Age: 65-68MY
Comment: I love that title – it makes it sound like they are getting important insights from a bag of bones sitting in a deck chair. Or that’s how I imagine it, anyway…
The evidence for the retina is *yawn* fossilised melanosomes, while the material that the ‘somes are imbedded in is mineralised.
We also have in other places evidence that is “suggestive of the presence of hemoglobin decomposition products, and thus indicative that the traces may represent residues of visceral organs derived from the decaying animal.” But their “SEM-EDX analysis demonstrated that the stained areas contain iron, oxygen and carbon, to suggest a partial replacement of the organic matter with either siderite or pyrite (which, in turn, may have altered to iron oxyhydroxides), i.e., diagenetic minerals commonly associated with exceptional soft tissue preservation.” So, not quite an impossible, complete original material survival case…

Why was I yawning about melanosomes? They don’t really count as preserved soft tissues – as I said in an earlier entry:

Another study on a similar topic says that “there is extensive evidence that melanosomes are highly resistant to chemical and physical degradation and have higher resistance to decay than the keratin substrate of feathers and hairs in a variety of physical environments.” These are solid organelles!

The other entry that Thomas could be talking about is this:

35. Microspectroscopic Evidence of Cretaceous Bone Proteins:

Authors: Johan Lindgren, Per Uvdal, Anders Engdahl, Andrew H. Lee, Carl Alwmark, Karl-Erik Bergquist, Einar Nilsson, Peter Ekström, Magnus Rasmussen, Desirée A. Douglas, Michael J. Polcyn, Louis L. Jacobs
Link: full text
ICR Description: C-14 date of Mosasaur (24,000 Yrs)
Age: 70MY
Comment: The C-14 date was usead as part of the proof that the collagen they found wasn’t from modern sources – it “most likely reflects bacterial activity near the outer surface of the bone”. Translating the amount of carbon into a date almost looks like an afterthought…
The collagen itself is interesting. As usual, they suggest plausible mechanisms for suvival, relating to inacessability from microbes etc. I can’t find any followup on this, though it looks reasonably solid.

I can’t quite remember what was going on with the carbon-14 date (it wont be accurate, I can tell you that), but they do propose a mechanism for the survival of the protein.

The next item is simply “amber insects.” The date matches with this entry:

4. Amino acid racemization in amber-entombed insects: Implications for DNA preservation:

Authors: Jeffrey L. Bada, Xueyun S. Wang, Hendrik N. Poinar, Svante Pääbo and George O. Poinar, Various
Link: abstract
ICR Description: Unaltered amino acids in amber insects
Age: 130MY
Comment: More amber… This particular study did tests on insects trapped in amber for times ranging from the 130 million years given right down to less than a hundred years. They determined that in amber the natural decay and modification of amino acids is reduced significantly over that in a test tube, hardly an argument against an old earth…
And, for that matter, since when are amino acids ‘soft tissue’? You can make them abiogenically, for goodness sake (not that that would affect the results here).
NB: This paper says that their “conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.” As I mentioned above, these reports were premature. But, if it ever turns out that we do find such DNA, it seems that it may not be so impossible. Whether we do or don’t, this paper stands on its own.

Most important here is that this has nothing to do with collagen, so it shouldn’t be on Thomas’ graph. This could be considered the equivalent of the Moa study, but on amino acids in amber. They just survive longer than you would think, that is all.

The next is the Psittacosaurus. This is most likely either:

18. A unique cross section through the skin of the dinosaur Psittacosaurus from China showing a complex fibre architecture:

Authors: Theagarten Lingham-Soliar, School of Biological and Conservation Sciences, University of KwaZulu-Natal Private Bag X54001, Durban 4000, Republic of South Africa
Link: full text
ICR Description: Psittacosaurus skin
Age: 125MY
Comment: Again, the “preserved tissue” has been mineralized – that is, properly fossilised and none of the original material remains.

Or:

28. The integument of Psittacosaurus from Liaoning Province, China: taphonomy, epidermal patterns and color of a ceratopsian dinosaur:

Authors: Lingham-Soliar T, Plodowski G, Biological and Conservation Sciences, Biological Sciences Building, University of KwaZulu-Natal, Westville Campus, P. Bag X54001, Durban, South Africa
Link: abstract
ICR Description: Psittacosaurus skin color
Age: 125MY
Comment: Lingham-Soliar and Plodowski’s counter to the above. They find melanosomes in their dinosaur aswell, and argue that that means that “decomposition of the skin releases pigments that readily permeate underlying structures” as nobody is aguing that Psittacosaurus had protofeathers. I don’t know how much direct evidence they have of the melanosomes in their fossil, and how they counter claims that the organells are in ordered arrangements, which had previously been used as part of the evidence that they were melanosomes and not bacteria as had previously been thought.
I can’t see anything that would make it a genuine impossible survival of orginal material case in this, as with the previous.

(This paper was one of a series on the “did birds evolve from dinosaurs” debate, talking about the preservation of evidence of “protofeathers.”) There is no collagen here, or indeed anything that justifies eithers inclusion on this graph.

Then we have the Seismosaur:

2. Preservation of the bone protein osteocalcin in dinosaurs:

Authors: Gerard Muyzer, Philip Sandberg, Marjo H.J. Knapen, Cees Vermeer, Matthew Collins and Peter Westbroek, various
Link: abstract
ICR Description: Osteocalcin in a seismeosaur bone
Age: 150MY
Comment: Interesting… It should be worth noting that, as with the Schweitzer dinosaur stuff, the authors of that paper are also suggesting how the protein could survive, this time having done actual experiments that demonstrate how different circumstances – such as being close to the bone – can wildly change protein survival rates. It is not clear that the protein could not have survived the time.

This isn’t collagen either, and it isn’t clear that survival for that long is impossible.

The final item is the eggs from last week, which among other problems don’t seem to be collagen either. We therefore have quite the mixed bag here, and Thomas’ graph is a rather misleading in including non-collagen finds in with those that are not of that nature. Also, if we’re allowed a difference of 400 times between lab results and reality, as with the DNA, we could easily fit all of these finds.

Now, Thomas himself goes on to say:

What are the odds that contamination infected so many varied fossil proteins from so many different places?

Yes, what are the odds that you could find seven – seven – examples of bones containing something that at least Thomas could mistake for soft tissues out of the millions of fossils that have been dug up? Imagine you rolled a thousand 6-sided dice, all at once. Would it be reasonable to count up all the sixes and say “There’s more than a hundred and fifty! How is that possible!?” I don’t think so – due to the nature of probability even quite impossible things become near-certainties given enough tries, and excluding all the failures in your analysis just makes you look foolish.

Thomas concludes:

Instead of following the evidence where it clearly leads, some use broom tactics to sweep away scientific challenges to secular beliefs. Sometimes human will—not reason—drives conclusions and behavior. Some ignore the fossils, ignore protein decay, or claim contamination. But all three tactics create far more problems than they solve. The most straightforward solution follows this fossil evidence straight to biblical origins in Noah’s recent Flood.

You’ll note that he again asserts that the “tactics create far more problems than they solve.” He never does explain what they are. Raising the possibility of contamination is just engaging proper scepticism and employing Occam’s razor, nothing more.

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7 thoughts on “What are the odds?

  1. What gets me everytime I read about these biomolecules as evidence of a young earth is that Brian doesn’t seem to ask the question, why are there as few biomolecules as there are? If these bones were preserved (under fast preservation conditions I might add) just 4000 years ago should every bone be full of biomolecules of all types. I mean, look at sabertooth cat bones where are by YEC accounts 3500 years old, there is plenty of biomolecules left in them and many other mammalian bones. It should be shocking to YECs that fossils are not more fresh than they are.

  2. I believe Eye on the ICR read and critiqued a few months’ back a peer-reviewed science paper which suggested how soft tissues could be preserved for millions of years (I forget the full details).

    “human will—not reason—drives conclusions and behaviour…”. And especially if you are YEC who has decided to believe that the Bible presents infallible science:
    http://freethoughtblogs.com/pharyngula/2013/05/15/the-stupid-problem/ (this is actually no better than crude YEC propaganda cartoons about evolutionists, but it seems pertinent as well as being new)

    I see that Georgia Purdom of AiG is flagging a dinosaur skin finding on her Facebook page:
    http://phys.org/news/2013-04-scientists-rare-dinosaur-skin-fossil.html#jCp

    • “I see that Georgia Purdom of AiG is flagging a dinosaur skin finding on her Facebook page:
      http://phys.org/news/2013-04-scientists-rare-dinosaur-skin-fossil.html#jCp

      Brian Thomas has now written a new post about this same story.
      http://www.icr.org/article/7523/

      According to the article which is flagged as his footnote 1: “Barbi said this is only the third three-dimensional dinosaur skin specimen ever found worldwide”. Would you not expect more such cases – if the dinosaurs perished in a massive flood 4,300 years’ ago, or perhaps much more recently than that?

      So does Mr Thomas comment on this? No, he does not.

      He highlights the mystery “But perhaps the greatest question Barbi is trying to answer at the CLS is how the fossil remained intact for around 70-million years”, cast doubt on this timescale because of scripture, and concludes with an insincere sounding “Good luck answering your greatest research question, Mauricio Barbi. Research that ignores the most sensible solution to the dinosaur skin dilemma signals a poor start”.

      Thomas asks a significant question but unfortunately fails to offer any kind of answer: “How long could actual dinosaur skin tissue possibly last?”. Presumably he would like a figure of around 5,000 years? Long enough to occasionally preserve skin from dinos which died in the flood or since but such that these are only rarely found preserved (he presumably would reject a figure of say 7,000 years – not because thatb would be impossible but because the time in question has ‘never’ elapsed’.

      Anyway, I’ll shut up now as Peter may be planning a blog post.

  3. If he doesn’t trust radiometric dating, preserved proteins etc. because scientists can just dismiss results they don’t like willy nilly as they can’t completely rule out contamination, why does he trust any other science. After all, they typically use p values of 0.05, so can’t rule out chance completely. They might just dismiss results they don’t like willy nilly to, so clearly can’t be trusted.

    Yet scientists only dismiss results when there is a good reason to (like lack of replicability raising the possibility that despite a low p value the result is still the product of chance). That’s why nobody uses his reasoning to reject every science ever. The thing is the same is also true of people who investigate preserved proteins etc.

    The only real difference is it’s a lot harder to arrive at the palaeontological equivalent of a low p value so you wind up with a lot more rejections of data. But that doesn’t mean it’s especially arbitrary

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