Forum:Proteins in bones

In this forum thread we discuss the proteins that have been found in dinosaurs fossils.

Progress we make in this thread should be included in the article: Proteins in bones.

Soft tissue
Have there been any independent studies outside of Schweitzer's team supporting the hypothesis that the proteins and tissues were endogenous? I know about the mosasaur and lufengosaur proteins, but what about the tyrannosaur collagen? Even today, with her studies, there seem to be a lot of skeptics. Here is an article on Wired about the controversy. According to the article, Asara and Schweitzer actually hid a lot of other protein data that matched up with ostrich hemoglobin, which had been studied before in their lab. Jurassic Park Treasury (talk) 05:25, July 23, 2013 (UTC)

Have there been any independent studies outside of Schweitzer's team supporting the hypothesis that the proteins and tissues were endogenous?

You answered your own question.

I know about the mosasaur and lufengosaur proteins

Schweitzer's published a new article in 2012 in which they identified new proteins and further proved that those proteins came from within the bone. Lindgren et al. (2011) also proved they found proteins INSIDE the bones.

what about the tyrannosaur collagen? Even today, with her studies, there seem to be a lot of skeptics.


 * Well, I've scanned the article a little. It is from 2009, which isn't really up to date. As I said, Schweitzer published a new article in 2012 which aimed to show that those proteins were endogenous. I'm pretty sure that it is now a consensus that those proteins are endogenous. If you can find criticism from a real scientific journal or magazines like Scientific American or NewScientist after 2011, I'll bother wasting a thought about it. BastionMonk (talk) 20:21, July 23, 2013 (UTC)

I copied some of the protein sequences from the 2012 paper and BLASTed them. Two of the Brachylophosaurus actin sequences matched with fungal actin. not bird or reptile actin. Fungi could contaminate the samples, even if the bones were underground.

The tyrannosaur collagen may have had similarity to birds, but it also had similarity to amphibians. I know protein code is conserved, but even that denies the fact that MAMMAL protein should have been more similar.

The more I investigate this, Schweitzer's methods become more and more pseudoscientific to me. However, the hadrosaur collagens do seem endogenous, since they only have a 60% or so similarity to modern birds. Then again, it also has a 70% similarity to mammals and a 59% similarity to bacteria, which doesn't make sense. It's probably not much to worry about, but still. I know you said that genes stopped evolving 500 million years ago, but bacteria and animals diverged much eariler than that. So why is a species of Bacillus showing up on the BLAST list?

At the same time, however, as you said, the collagen came from within the bone. And you said BLAST was a crude method. Are there any better ones out there?

Jurassic Park Treasury (talk) 03:22, July 24, 2013 (UTC)

I copied some of the protein sequences from the 2012 paper and BLASTed them.

The sequences are VERY short, making comparisons doubtfull.

This is what they wrote:

These data support the presence of non-microbial DNA in these dinosaur cells. Actin, tubulin, and histone H4 are all highly conserved, essentially identical over all animals (Bilateria), and indeed the detected sequences for T. rex and B. canadensis are identical to the consensus sequence.

Could you show the results for each sequence. Since they are so short, I can't believe there is that much difference between them. If one peptide is different, you can immediately have an 90% difference. Which is just noise.

Then again, it also has a 70% similarity to mammals and a 59% similarity to bacteria, which doesn't make sense.

That perfectly makes sense. The proteins are very conserved throughout all life-forms. It would have been weird is it had 70% similarity with bacteria and 50% with animals.

I know protein code is conserved, but even that denies the fact that MAMMAL protein should have been more similar.

No, it isn't.

Schweitzer's methods become more and more pseudoscientific to me.

You have no right whatsoever to say that. Their methods are very good. You can argue whether their interpretations are right. BastionMonk (talk) 09:21, July 24, 2013 (UTC)

I copied some of the protein sequences from the 2012 paper and BLASTed them. Two of the Brachylophosaurus actin sequences matched with fungal actin. not bird or reptile actin.

I've done a couple of BLAST myself and listed them below. The sequences are 100% in ALLL life forms. 100% similar to fungi, insects and humans. These regions are conserved throughout evolution. Nothing to worry about. They said this in the article.

Can you please stop freaking out like this and take your time to carefully look at results. BastionMonk (talk) 09:54, July 24, 2013 (UTC)

Actin
Sequence:

AGFAGDDAPR


 * BLAST: 100% identical to all sequences in GenBank, including Cladosporium, Mycosphaerella, Trichophyton, Colletotrichum and again Cladosporium.
 * Interpretation: Sequence remained 100% identical throughout evolution, since it is identical in fungi, bony fish, bivalves and rodents. If this is a dinosaur protein, this sequence is what we would expect to see.


 * However, fungi still make up the majority of the list. Jurassic Park Treasury (talk) 04:28, July 25, 2013 (UTC)


 * All sequences are 100% identical, so I don't think that matters. BastionMonk (talk) 08:02, July 25, 2013 (UTC)
 * You're right. I searched for the same sequence in reptiles and birds and it was still there. It also helps us know what type of actin it is. I think it is alpha actin because all sequences from the reptiles and birds that showed the AGFAGDDAPR sequence were labelled as that. Jurassic Park Treasury (talk) 09:36, July 25, 2013 (UTC)

Sequence:

AVFPSIVGR


 * BLAST: matches 100% with creatures ranging from Humans to.
 * Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see.

alpha-1A
Sequence:

QXXXXXXXXXXXXXXXXLFHPEQLITGK


 * BLAST: matches 100% with creatures ranging from Humans to.
 * Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see.

Sequence:

EIIDLVLDR


 * BLAST: matches 100% with creatures ranging from Humans to.
 * Interpretation: This sequence is conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see.

Histone H4
Sequence:

DAVTYTEHAK


 * BLAST: 100% identical to all sequences stored in GenBank (couldn't find vertebrates though)
 * Interpretation: This sequence is probably conserved in all life forms. If this is a dinosaur protein, this is what we would expect to see.

Amino Acid sequence:

1 gatgapgiag apgfpgarga pgpqgpsgap gpkxxxxxxx xxxxxxxxxx xxxxxxxxxx 61 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 121 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 181 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 241 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxgv qgppgpqgpr 301 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 361 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 421 xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxgs agppgatgfp 481 gaagrxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx xxxxxxxxxx 541 xxxxxxxxxx xxxxxxxxxx xgvvglpgqr


 * BLAST: Has a 94% similarity to chickens, sea turtles and amphibians, with a 91% similarity to anoles and mammals.
 * Interpretation: Looking at the BLAST list more closely, this sequence does seem to be endogenous. If this is a dinosaur protein, then the similarity to modern archosaurs is what we'd expect to see.

Collagen, type I, alpha 2
Amino Acid sequence :

glpgesgavg pagpigsr
 * BLAST: 100% identity with modern birds, including ducks, pigeons, finches, chickens and collared flycatchers. 94% identity with mammals, and an 88% identity to lizards.


 * Interpretation: This protein seems to be highly conserved in birds. Since T. rex and birds are both coelurosaurs, I'll give it the benefit of the doubt, but it's a bit hard to tell without sequences from other groups of modern archosaurs first.

Amino Acid sequence :

gsngepgsag ppgpaglrgl pgesgavgpa gppgsr
 * BLAST: 67% identity with chickens, ducks, pigeons and turkeys, and a 76% identity with anoles.


 * Interpretation: This protein seems to be similar throughout all amniotes (reptiles, mammals and birds). If it is a dinosaur protein, the similarity with birds and lizards is what we would expect to see.

Amino Acid sequence :

1 glvgapglrg lpgk
 * BLAST: 100% identity with Xenopus, AKA the African clawed frog.


 * Interpretation: Oh dear, this one seems more disappointing. Although Schweitzer and Horner said that there were no amphibians in the Hell Creek area, African clawed frogs are common model organisms in labs.

Amino Acid sequence :

1 gatgapgiag apgfpgargp sgpqgpsgap gpkgvqgppg pqgprgltgp igppgpagap 61 gdkgeagpsg ppgptgargs agppgatgfp gaagrgetgp agpagppgpa gar


 * BLAST: 60% identity with chickens, 56% with sea turtles, 58% with anoles, 63% identity with armadillos.
 * Interpretation: This protein sequence doesn't seem to be as conserved as the others. Due to the better sterilization techniques used for Brachylophosaurus, and the fact that no modern sequence has an exact match to it, I'd say that this is a dinosaur protein.

I blasted the rex collagen again, now it also has a 94% similarity to peregrine falcon and painted turtle proteins. This helps confirm the hypothesis that it is endogenous. Jurassic Park Treasury (talk) 06:59, September 9, 2013 (UTC)

I BLASTed the T. rex COL1A1, looking for similarities in amphibians only. It had a 100% similarity with Xenopus. Not only is this completely identical, it is higher than the similarity to birds and reptiles.

The debate is over. The proteins are contamination. Needless to say, I'm disappointed. Jurassic Park Treasury (talk) 02:09, December 5, 2013 (UTC)

EDIT: It seems that BLAST search only covers one part of the sequence. Other parts weren't 100% identical. Bastion, I know you told me to stop freaking out, but I just have a skeptical mind.

I know you said the proteins were found inside the bones, but that doesn't rule out contamination if another animal's proteins got inside the bone through reusing used tools. Jurassic Park Treasury (talk) 02:22, December 5, 2013 (UTC)