Pharyngula

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Thursday, March 24, 2005

Tyrannosaur morsels

Look! A scrap of soft tissue extracted from dinosaur bone:

Tyrannosaur soft tissue
Demineralized fragments of endosteally derived tissues lining the marrow cavity of the T. rex femur. The demineralized fragment is flexible and resilient and, when stretched (arrow), returns to its original shape.

Dr GH has already promised to describe this new find in more detail on The Panda's Thumb, so I'm going to be very brief—keep an eye on The Thumb for more.

Anyway, it has been reported in Science this week that well-preserved soft tissues have been found deep within the bones of a T. rex, and also within some hadrosaur fossils. This is amazing stuff; fine structure has been known to be preserved to this level of detail before, but these specimens also show signs of retaining at least some of their organic composition. What the authors have done is to carefully dissolve away the mineral matrix of the bone, exposing delicate and still flexible scraps of tissue inside.

Here, for example, is a piece of endothelial tissue, or the tubelike epithelia that line blood vessels and form capillaries. It is compared to a similarly prepared piece from fresh ostrich bone; you can tell the T. rex fragment has undergone some changes, but it's comparable in size and organization to the bird sample.

Tyrannosaur soft tissue
(I) T. rex vessel fragment showing detail of branching pattern and structures morphologically consistent with endothelial cell nuclei (arrows) in vessel wall. (J) Ostrich blood vessel liberated from demineralized bone after treatment with collagenase shows branching pattern and clearly visible endothelial nuclei.

Looking more closely with a scanning electron microscope, here's a similar piece of T. rex blood vessel that has ruptured, spilling out its contents. Maybe those cells don't look perfectly preserved, but they're darned close.

Tyrannosaur soft tissue
Exploded T. rex vessel showing small round microstructures partially embedded in internal vessel walls.

And lastly, here's a closeup of the surface of that epithelia, compared with an ostrich epithelium. The cells here are very, very flat, and the nuclei are the thickest part, bulging up and giving the surface a pebbled appearance. The T. rex epithelium has a similar pebbly look, suggesting that just maybe there is even some subcellular structure preserved.

Tyrannosaur soft tissue
(E) Higher magnification of a portion of T. rex vessel wall, showing hypothesized endothelial nuclei (EN). (F) Similar structures visible on fixed ostrich vessel. Striations are seen in both (E) and (F) that may represent endothelial cell junctions or alternatively may be artifacts of the fixation/dehydration process.

How could this be? Here's the authors' explanation.

…we demonstrate the retention of pliable soft-tissue blood vessels with contents that are capable of being liberated from the bone matrix, while still retaining their flexibility, resilience, original hollow nature, and three-dimensionality. Additionally, we can isolate three-dimensional osteocytes with internal cellular contents and intact, supple filipodia that float freely in solution. This T. rex also contains flexible and fibrillar bone matrices that retain elasticity. The unusual preservation of the originally organic matrix may be due in part to the dense mineralization of dinosaur bone, because a certain portion of the organic matrix within extant bone is intracrystalline and therefore extremely resistant to degradation. These factors, combined with as yet undetermined geochemical and environmental factors, presumably also contribute to the preservation of soft-tissue vessels. Because they have not been embedded or subjected to other chemical treatments, the cells and vessels are capable of being analyzed further for the persistence of molecular or other chemical information.

So, basically, these cells were entombed in a thick mineral sarcophagus, protected from bacteria and other external insults. There have to have been other factors at play—cells are full of enzymes that trigger a very thorough self-destruct sequence at death—so I'm definitely looking forward to the molecular analysis. Even if their form was preserved, I expect these cells to be denatured monomer soup on the inside.


Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK (2005) Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex. Science 307(5717):1952-1955.


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Comments:
's avatar #19879: Ben — 03/26  at  10:15 AM
Both sides have assumptions.

Alright, let's hear 'em. I'm in a patient mood.

You indicated that the result was arbitrary because of the choice of method.

Um, I've said about four fucking times now that the results are arbitrary because the source (ie, the data) is assumed to have anything to do with the issue, in this case the cast of Biblical characters with the age of the planet. Would you like me to say it a fifth time? Fuck it, I'll just copy/paste what I originally wrote.

<style illusion? Skyhooks, my friend.</blockquote>

I'm glad that you realise that the accuracy of the data is important. Now explain how you can tell how any of the Biblical data you're using is accurate. THEN tell me hwo it's pertinant to cosmology. WITHOUT using the words "belief" or "faith", and without circular logic. If you can't, then you're blatantly contradicting yourself.

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



's avatar #19880: Ben — 03/26  at  10:19 AM
Now you know why I don't use blockquotes very often.

<style illusion? Skyhooks, my friend. </blockquote>

And another thing...

Nice analogy! So you've never known a clock to be wrong?

You dump on his analogy, then you make a dick of yourself by using it in a totally ridiculous way? Sure, the radioisotopic decay stops when the rock's battery goes flat. Moron.

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



's avatar #19881: Ben — 03/26  at  10:23 AM
Now you know why I never use blockquotes.

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



's avatar #19883: Chris Clarke — 03/26  at  10:37 AM
<blockheadquote>That depends on your paradigm—uniformitarianism or creationism.</blockheadquote>

Homework for PJ Rayment: write a two-paragraph essay explaining why the above sentence proves you have no idea what you're talking about.

"I do not think we should antagonize the religious when it is not warranted, though I think we should be willing to do so whenever it is.”
-- Glen Davidson



's avatar #19884: PZ Myers — 03/26  at  10:40 AM
Do I get to grade these homework assignments?

PZ Myers
Division of Science and Math
University of Minnesota, Morris



's avatar #19885: Chris Clarke — 03/26  at  10:43 AM
I was assuming they'd be juried. But if you don't have enough homework to grade, have at it... assuming any of them ever turn in any of their assignments.

"I do not think we should antagonize the religious when it is not warranted, though I think we should be willing to do so whenever it is.”
-- Glen Davidson



#19889: Hank Fox — 03/26  at  12:04 PM
"The examples I would quote are ones from AiG [...]. No, I'm not making them up, and neither is AiG. Most if not all the dates they quote are calculated by secular laboratories ..."

Ahem. SECULAR laboratories?

I wonder why they used SECULAR laboratories? I mean, hey, if you're making a Christian argument, why not use laboratories run by CHRISTIAN Scientists?



#19890: Hank Fox — 03/26  at  12:09 PM
Hey, Philip, you know what?

Ain't nobody here who has the JOB of educating you. All the knowledge, all the information, is out there. It's as close as your nearest library. There’s probably nearby junior high school students who could explain this stuff to you.

The real problem here is that if there's a brightly-lit place somewhere on Earth where only the truth gets told, you're a thousand miles away in the darkness. Telling lies, talking nonsense.

You're flat-out WRONG. Not because of anything any one person here says, but because you’re actually FIGHTING TO FAIL TO UNDERSTAND THE FACTS.

And because you think WINNING an argument, cowing your opposition, is what determines the truth of the proposition under discussion.

That's just dumb as all hell, boy.

Yeah, yeah, I’m sure you're going to go away from here telling yourself "I sure showed those atheist science assholes a thing or two."

But I hope you don’t. Because you didn’t show anybody anything. You defeated yourself. You’re continuing to defeat yourself, because you DON’T WANT TO LEARN anything about the subject under discussion.

You’re afraid.

For some reason, you find this field of knowledge threatening. And that’s the REAL challenge you face, bucko.

The question is not “Why can’t I make these people understand?” The real question is “What have I let into my head that’s made me so afraid?”

Really.



#19907: — 03/26  at  01:55 PM
Hank that was a first rate summary of the situation.

It was really hard to keep reading:

"Your data may be wrong since you pulled it from a fairy tale", Ben.
"My method is not wrong. My data cant be wrong because I already said that bad data produces bad results. My method is not wrong", PJR

repeat..

Ben, please finish them off quicker in the future. I hate watching cats play with mice instead of just eating them. Well maybe not in a metaphorical sense.



#19908: — 03/26  at  01:55 PM
Philip scrawled:

More bluster, no substance.


Phillp, me lad, you've stepped into it here. You have blustered on about "assumptions", even quoting from Talk Origins. The problem you have overlooked is that at the end of the day, assumptions must be testable. The radiometric ages determined for rocks must agree with the relative ages determined for the same rocks. Isochron plots are diagnostic diagrams that allow us to test if assumptions of lack of original daughter, or loss of radiogenic daughter hold up.

The typical YEC claims about 'incorrect' radiometric dates in the literature are yet classic examples of the rank dishonesty among creationists:

http://www.talkorigins.org/faqs/woodmorappe-geochronology.html

I swear, creationist Bibles must be leaving out the 9th commandment!



#19926: — 03/26  at  03:34 PM
Philip Rayment: " It(the age of the earth = 6k years) is derived by adding the ages of Biblical characters..."

Gen1:1 "God created the heavens and the earth"
Gen1:16 " Then God made two great lights... He made the stars also."

Look up at the night sky and pick out any deep space object, say M31. The light that forms the image of that galaxy in your brain left that galaxy over 2 million years ago. And since the Bible says the earth was created BEFORE the stars, then the earth is AT LEAST 2 million years old, NOT 6000.



#19927: coturnix — 03/26  at  03:43 PM
Nice sarcastic letter to the editor:

http://www.newsobserver.com/opinion/story/2253732p-8633667c.html



#19941: — 03/26  at  06:19 PM
Phillip, what kind of catastrophe could've possibly fossilized such remains in a very short timespan without destroying them completely?

You wrote the alleged date of creation is derived by adding the ages of Biblical characters when they had their offspring. And that makes perfect mathematical sense

That's sheer BS. The date -- supposedly, 4004 BC -- came from Bishop James Usshar of Armagh, Ireland, in the 1600s. It's pure fiction, even using the ages given in Genesis.

Have you ever actually tried ADDING the numbers in Genesis together? I have. If you assume a starting date of about 1300 BCE (when the historical record can document early Hebrew occupation of Israel, clearly something that had to happen BEFORE Genesis was written down) and work back from there, adding the numbers together takes you back over 8000 years. In other words, not 6000 years ago, but over 11,000 years ago. Logically, you'd also have to add more time to account for the many years Genesis must've been an oral story before it was first written, but we have no way to know how long that was.

Why should we listen to YOU when you can't even check your own "facts", never mind accept other sources of evidence that the writers of that book simply didn't know about then? They were ignorant, but not by choice.

Genesis is simply one culture's story of how they believed they came to be in the world, just like thousands of others worldwide. The fact that it's known by far more people than most other myths and written in a very popular (and badly edited) book does not make it true.



's avatar #19943: PZ Myers — 03/26  at  06:36 PM
What's more, the infamous date of 4004 BC did not come from adding up the ages of the patriarchs -- it's numerology, pure and simple. Just as there were 7 days in the Creation, there were to be 7 ages of a thousand years each, culminating in the Apocalypse or whatever and a last thousand year kingdom with Jesus back in the saddle. Why 4004 BC? Because Jesus was supposedly born in 4 BC, and all the ages are supposed to be precisely a thousand years long, with 4 ages preceding him.

All sorts of funky wild stuff should have hit the fan in 1996. I missed it.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



's avatar #19952: Ben — 03/26  at  07:43 PM
Given the time he said he had to go to bed, I get the feeling he's in my approximate time zone (unless he's nocturnal). I forgot that it's Easter Sunday and they're all probably at church now. Damn. I should've slept in.

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



#20000: — 03/27  at  01:44 AM
Reading the posts, I feel the creationists above have succeeded in drawing the discussion into a place we have nothing to do. They caused serious scientists compute the generations of Adam and the position of the stars at the first day of Creation. It is ridiculous. PZ is right: this issue was settled a hundred years ago, and no scientist with a minimum of self-respect keeps discussing with people who do not bother to study the basics.

On the other hand, I read the Wedge Project of Discovery Institute, and it is a serious effort that has to be addressed. The basic argument is that the godless, materialistic culture of the 19th Century has generated a hellish 20th Century, so better we go back to former religious ideologies. At this time, more than negating evolutionary biology and other natural sciences, they want to make a place for religions based on the Bible. Scientists debating biblical chronology is what they intend to achieve at this time. The Wedge Project is attacking science and strives to introduce doubt in its completeness not because they find fault with science in itself but because they think its political consequences are bad. They are a political or social movement and the battleground is neither on the science ground nor on the biblical literalicy, but on the political arena.



#20017: — 03/27  at  08:37 AM
Ben wrote:
Both sides have assumptions.

Alright, let's hear 'em. I'm in a patient mood.
I'm not about to attempt to list them all, but for starters, creationists assume that the Bible is true, and evolutionists assume that uniformitarianism is true. Both also assume that our senses are reliable enough to study this stuff.

Ben wrote:
Nice analogy! So you've never known a clock to be wrong?

You dump on his analogy, then you make a [deleted] of yourself by using it in a totally ridiculous way? Sure, the radioisotopic decay stops when the rock's battery goes flat. Moron.
There are other ways a clock can be wrong. Something might interfere with the mechanism. It might not have been set to the correct time to start with. There's other possibilities also.

"Most if not all the dates they quote are calculated by secular laboratories ..." Ahem. SECULAR laboratories?

I wonder why they used SECULAR laboratories? I mean, hey, if you're making a Christian argument, why not use laboratories run by CHRISTIAN Scientists?
Because you blokes would immediately jump on that and say that creationists invented their own figures. But if they used figures from sources accepted by non-creationists, it makes it harder for you to reject them (or you look sillier doing so).

Hank Fox wrote an extended piece in which he attempts to read my mind and discover my motives. It added nothing to the discussion except insults and unfounded (and incorrect) speculation.

Neil wrote:
The problem you have overlooked is that at the end of the day, assumptions must be testable.
Then they wouldn't be assumptions. Some assumptions are simply not testable, so they must remain assumptions.

Neil wrote:
The typical YEC claims about 'incorrect' radiometric dates in the literature are yet classic examples of the rank dishonesty among creationists:
The link was to a paper that disagreed with a creationist paper, and although the author did accuse this particular creationist of not being fully honest, the thrust was not primarily of dishonesty and certainly not "rank dishonesty".

SteveR wrote:
Look up at the night sky and pick out any deep space object, say M31. The light that forms the image of that galaxy in your brain left that galaxy over 2 million years ago. And since the Bible says the earth was created BEFORE the stars, then the earth is AT LEAST 2 million years old, NOT 6000.
The stars are over 2 million light-years away, but that is a measure of distance, not time. It only becomes a measure of time with some assumptions, such as the constancy of the speed of light over time (which I am not disagreeing with to any significant extent) and, more generally, the whole Big Bang hypothesis. Creationist cosmologies that explain that apparent paradox have been developed, but that is really getting off the subject.


Gus wrote:
You wrote the alleged date of creation is derived by adding the ages of Biblical characters when they had their offspring. And that makes perfect mathematical sense

That's sheer [deleted]. The date -- supposedly, 4004 BC -- came from Bishop James Usshar of Armagh, Ireland, in the 1600s. It's pure fiction, even using the ages given in Genesis.
Archbishop Ussher—just one of many people to come up with a similar date—derived his date by the method I described.

Gus wrote:
Have you ever actually tried ADDING the numbers in Genesis together? I have. If you assume a starting date of about 1300 BCE ... and work back from there, adding the numbers together takes you back over 8000 years.
I don't know how you got that figure (perhaps you added their ages at death instead of their ages at the birth of their offspring?) See here for the actual figures. From Adam to Abraham adds up to just over 2000 years.

Gus added:
Why should we listen to YOU when you can't even check your own "facts", ...
Hmmm.

PZ Myers wrote:
What's more, the infamous date of 4004 BC did not come from adding up the ages of the patriarchs...
Yes it did. Adding their ages at the births of their offspring is precisely how Ussher did it.

jaimito wrote:
Reading the posts, I feel the creationists above have succeeded in drawing the discussion into a place we have nothing to do.
Creationists? I've not noticed any others. Anyway, it wouldn't have gone this way if several different anti-creationists didn't bring creationary beliefs into the discussion in a derisory way.



#20037: kelley b. — 03/27  at  11:43 AM
Umm... back to dinosaur bone marrow preserved after 65 million years in an oxidizing atmosphere...

I'm very skeptical about this.

Yes, it's soft tissue of something.

I think they should go in there and do some PCR with conserved primers or mass spec peptide sequencing and do a BLAST at NCBI.

That might be a little more revealing as to what critter this tissue is really from.



#20072: — 03/27  at  01:41 PM
Phillip, you don't seem to be grasping one fundamental fact:

When you're in a hole, stop digging.

Then they wouldn't be assumptions. Some assumptions are simply not testable, so they must remain assumptions.


Oooooookkkkkayy...so, when plotting isotope ratios on an isochron diagram, we assume that there was no original daughter and that there was no loss of radiometric daughter. When there are enough points, we test these assumptions by fitting the isochron. If it's a straight line, the assumptions have been tested and (pending further data) are valid. If there's scatter, then the assumptions weren't valid.

Ultimately, we make assumptions to get a result that can be compared with reality. That comparison is the test of the assumptions. This is a concept I readily explain to bright HS students. Let's stay with the program, eh?

The link was to a paper that disagreed with a creationist paper, and although the author did accuse this particular creationist of not being fully honest, the thrust was not primarily of dishonesty and certainly not "rank dishonesty".


Quotes from Schimmrich's paper on Woodmorappe's work (each is from a different section):

"This is a deliberate misquotation of McKee and Noble and this example alone would be enough to prevent publication of this paper in any reputable scientific journal."

"Woodmorappe's quotation of Wasserburg and Lanphere's work was incomplete and misleading."

"Therefore, this data point does not, in any way, support Woodmorappe's thesis that present-day techniques of radiometric dating are unreliable."

"Why didn't Woodmorappe discuss the 40 glauconite dates listed in the data table of this paper that were well within 10% of the expected geologic age?"

"...but if he accuses the authors of "fudging" data he has a responsibility to at least discuss it and to explain why he disagrees."

"The large amount of evidence carefully discussed and referenced by Higgins was totally ignored as if it never existed."

Keep in mind the author of the review is an evangelical Christian! Once or twice might be an honest mistake, but repeated like this it is clearly a case of, uh, design. If I were to receive a paper to review with analogous problems, I'd be on the phone to the editor in an instant.



's avatar #20073: Chris Clarke — 03/27  at  01:45 PM
evolutionists assume that uniformitarianism is true.


Wrong.

It would help your credibility immensely if you stopped arguing against 19th-century science.

OK, no it wouldn't. But it would give people who know what they're talkiing about one less reason to write you off as an ignorant fool.

"I do not think we should antagonize the religious when it is not warranted, though I think we should be willing to do so whenever it is.”
-- Glen Davidson



#20091: — 03/27  at  03:28 PM
Philip J. Rament writes: "It only becomes a measure of time with some assumptions, such as the constancy of the speed of light over time (which I am not disagreeing with to any significant extent)..."

If you're not disagreeing, then IT IS a measure of time. And don't forget, I picked a relatively close messier object. 'Slight variations in the speed of light' could easily be overcome by selecting much more distant objects.

Philip J. Rament: " Creationist cosmologies that explain that apparent paradox have been developed .."

I'd be interested to know what they are. Can you provide links?



's avatar #20111: Ben — 03/27  at  06:13 PM
I'm not about to attempt to list them all, but for starters, creationists assume that the Bible is true, and evolutionists assume that uniformitarianism is true. Both also assume that our senses are reliable enough to study this stuff.

Even if you're right about uniformitarianism (which you're not), don't creationists always rely on that one extra assumption? You also have to "rely" on uniformitarianism, and the reliability of your own senses. Why not use Occham's Razor to slice that superfluous assumption away?

It's all a moot point, however. Your uniformitarianism charge is a lie, and the "reliability of the senses" canard has been debunked by me and others in previous entries as unfalsifiable.

There are other ways a clock can be wrong. Something might interfere with the mechanism. It might not have been set to the correct time to start with. There's other possibilities also.

That's the problem with analogies. They're often the most expedient method of proving beyond all doubt that you have no idea what you're talking about.

Is this the best you can do? Isn't lying a sin in that dusty old book you claim to be the complete moral, historical and scientific history of the universe? I recommend abandoning your little tangent of ignorance and starting all over again. Present your case for the scientific nature of creationism, and we'll start taking it seriously. Until then, it remains a figment of the collective religious imagination whose sole aim is to sucker in gullible fools like yourself.

Now are you unwilling to present that case for creationism without lying, or unable?

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



#20140: — 03/27  at  10:03 PM
Ussher not only determined the age of Creation in years, he also asserted that it began at 9:30 a.m.

Hard to derive that by summing up the length of the generations, unless he had copies of all the birth certificates.



's avatar #20144: Ben — 03/27  at  10:17 PM
Is that Greenwich Mean Time?

"The great trouble is that the preachers get the children from six to seven years of age and then it is almost impossible to do anything with them." --Thomas Edison.



#20181: — 03/28  at  08:18 AM
Neil wrote:
Phillip, you don't seem to be grasping one fundamental fact:

When you're in a hole, stop digging.
But I'm not in a hole. Just because you blokes look down on me doesn't mean I'm in a hole.

Neil wrote:
Oooooookkkkkayy...so, when plotting isotope ratios on an isochron diagram, we assume that there was no original daughter and that there was no loss of radiometric daughter. When there are enough points, we test these assumptions by fitting the isochron. If it's a straight line, the assumptions have been tested and (pending further data) are valid.
That's the theory, but it's not that straightforward in practice. See here.

Neil wrote:
Quotes from Schimmrich's paper on Woodmorappe's work (each is from a different section):
Only one of the quotes you gave actually indicate dishonesty (as opposed to, say, inadequate treatment), and that one claimed "deliberate misquotation", without any proof that the misquotation was in fact deliberate.

SteveR wrote:
Philip J. Rament writes: "It only becomes a measure of time with some assumptions, such as the constancy of the speed of light over time (which I am not disagreeing with to any significant extent)..."

If you're not disagreeing, then IT IS a measure of time.
Perhaps, but not necessarily the way you think. See my answer to your next question.

SteveR wrote:
Philip J. Rament: " Creationist cosmologies that explain that apparent paradox have been developed .."

I'd be interested to know what they are. Can you provide links?
See How can we see distant stars in a young universe? and A new cosmology: solution to the starlight travel time problem.

Ben wrote:
Even if you're right about uniformitarianism (which you're not), don't creationists always rely on that one extra assumption? You also have to "rely" on uniformitarianism, and the reliability of your own senses. Why not use Occham's Razor to slice that superfluous assumption away?
Huh? How is the reliability of our senses superfluous? Why do creationists have to "rely" (your quotes) on uniformitarianism? And how am I wrong about uniformitarianism?

Ben wrote
It's all a moot point, however. Your uniformitarianism charge is a lie, and the "reliability of the senses" canard has been debunked by me and others in previous entries as unfalsifiable.
My uniformitarian charge is not a lie. Even if I am wrong (which I don't believe I am), I am not lying about it. I never saw any debunking of the reliability of the senses claim, and yes, it is unfalsifiable, which is why it in an assumption rather than a provable fact.

Ben wrote:
Present your case for the scientific nature of creationism, and we'll start taking it seriously. ... Now are you unwilling to present that case for creationism without lying, or unable?
If you are prepared to be civil an not accuse me of lying when you have no valid reason for claiming that, I am prepared to do that via e-mail if you wish to contact me that way. But this page is not the place for that.

Harry Eagar wrote:
Ussher not only determined the age of Creation in years, he also asserted that it began at 9:30 a.m.

Hard to derive that by summing up the length of the generations, unless he had copies of all the birth certificates.
Ussher actually suggested nightfall, not 9:30 a.m. He derived the year by adding the ages at childbirth (although he did use some other time periods for later stages), but other methods for determining the likely time and date of that year. Wikipedia's article is, as far as I know, accurate on this subject.



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