110M-year-old dinosaur discovered with skin and soft tissue | Hacker News Reader

110M-year-old dinosaur discovered with skin and soft tissue

nationalgeographic.com

479 pointsvwcx110 comments

Hey, I'm the journalist who wrote the story. A few things: - The organic-rich film preserving the outlines of scales (so, yes, fossilized skin) is only a few millimeters thick. So Mitchell had to prepare the fossil extremely slowly in order to follow the film through the matrix. - The half-life of DNA is ~521 years at 13.1°C, as found in this 2012 paper: http://rspb.royalsocietypublishing.org/content/279/1748/4724 The team's model predicts higher half-lifes at truly freezing temperatures, but even at the extreme end, there's no way DNA would survive 110 million years. - The dating on the site is well constrained to ~110 million years old. The fossil was found in the Wabiskaw Member of the Clearwater Formation, a well-dated rock formation in Alberta. The underlying oil sands have been radiometrically dated to 112±5.3 million years old. (http://science.sciencemag.org/content/308/5726/1293)

Really awesome writeup of the find. Is Suncor going to be doing any additional, and somewhat more reserved, excavating to understand whether or not there are other important fossils nearby?

Thanks. Interestingly, this is the first large fossil like this that Suncor had run across, in all the digging they had done up in the oil sands. And as you can imagine, finding a land animal like this nodosaur in the middle of what would've been a shallow sea is extraordinarily unlikely. Other mining companies have found other fossils in similar formations, though usually of non-dinosaur marine reptiles (e.g. http://www.sciencemag.org/news/2016/10/ancient-sea-monster-b...).

How much does the DNA degrade (i.e., what does half life mean)? Would it be possible to align any preserved short sequences back together?

If the DNA strands keep getting chopped in half then eventually the strands will be too short to extract anything useful.

What zbyte64 said. Once the animal dies, the enzymes that constantly fix and error-check DNA are no longer around. DNA then degrades over time, cleaving in half every ~521 years on average. So past a million years or two, the fragments are so small, meaningfully putting them back together would be an impossible task, like reconstructing a porcelain bowl you had ground into dust.

Yes, but it is a statistical process. There are many copies of the DNA, so some fragments might still be useful (?)

So, if we assume that the dinosaur has 1 billion base pairs in its genome (huge assumption, see my other comment), it has degraded over 110 million years with a half life of 512 years, there is functionally 0 base pairs left[1] in each dna helix. Even statics can't help much there! I'm wide open to the possibility that I am incredibly wrong in any one of these assumptions however

[1] - http://www.calculator.net/half-life-calculator.html?type=1&n...

I didn't actually look into this or any of the references but I suspect the half-life model is not appropriate in the extreme case. That is, it's an approximation that works on a certain non pathological scale like newtonian physics. Probably need the quantum mechanics version for this.

Not if this really is well-described by independent probabilities, i.e., a chance of being preserved that falls exponentially in time. Even if after 1 million years only half of the strands of DNA have had all their info destroyed, and even if (very unrealistically), the ones that haven't been destroyed are completely intact, then after 100 million years you would need to start with 2^100 = 10^30 DNA strands to have a single one last. And there are < 10^18 cells in a land animal.

No, the only way for something to survive is if the half life model breaks down and the chance of decay during different time periods isn't independent. This would be the case if one of the strands was somehow preserved accidentally.

Yes, but you need fragments of only about 50 basepairs to assemble a genome (or a big part of it) back. A typical DNA strand has on the order of hundreds of millions of basepairs.

The point is that an entire genome (not just 50bp segments) is destroyed in 1 million years.

Why would this be an exponential process? The error is per base pair per unit time. If a DNA fragment is split cleanly in half, each half should have double the expected time to failure as the whole, because there is half the number of base pairs each with the same likelihood of error as before.

It's just like nuclear atomic decay. For each base pair, there is a small chance of decay each small time step. The chance of any given base pair remaining undecayed through some time T is the product of all those probabilities, which fall exponentially in T. The expected number of total surviving base pair is also exponentially falling.

People are talking about two different things in this thread, and that's why people are talking past each other. Some people think halving means "half the number of base pairs remain" which would be an exponential process, yes. The other group thinks that "halving" means literally cut in half -- a failed base pair cuts the DNA strand into two pieces. That would be a linear decay process. As someone with no understanding of the underlying decay processes it's not obvious to me which one is right.

Yes, but 100 million years is quite a few 521-year half lifes.

That half-life is the time it takes for the link between half of the bonds between nucleotides to break (http://www.nature.com/news/dna-has-a-521-year-half-life-1.11...)

So, after 1042 years, only a quarter of the bonds will be intact. After 100 million years, only 1 in every 2^190000 bonds will be expected to still be intact. Taking 2^10 = 1000, that's 1 in every 10^57000. I think that's quite a bit higher than our estimate for the number of particles in the universe (https://www.quora.com/How-many-particles-are-there-in-the-un...)

TL/DR: I wouldn't bet on it.

Mmmm that's not what half-life means. Half-life means that in 521 years, half of the DNA is "gone", not cut in half.

I'm not sure if you're being sarcastic or not...

Edit: Wow a lot of bs going on in the comments. First of all, there's an immense number of ways a DNA strand can degrade, and only one of them splits the strand in two. The relative importance of all these pathways depend on the environment of the DNA, which obviously changes for each and every fossil you have. The global kinetics of "DNA degradation" are supposedly first-order, which implies constant half-life.

http://rspb.royalsocietypublishing.org/content/279/1748/4724

> The relative importance of all these pathways depend on the environment of the DNA, which obviously changes for each and every fossil you have.

And I guess it might for every cell of a single fossil.

How would you know where to align the sequences? I am not an evolutionary biologist so maybe one of those people have a "yes, actually!", but consider modern descendants of dinosaurs have 1 billion base pairs and 20,000-23,000 genes[1], and the fact that we have many many living versions of those fowl to experiment with. Trying to realign chopped up bits of dna with who know how much completely missing, and minimal opportunities to experiment or direct information as to how any particular sequence functions, I can't see any way to extract useful data from highly degraded dna.

More information of degraded dna handling techniques, albeit in the forensics field and aimed toward people, but interesting to me nonetheless [2]

[1] - http://www.nature.com/nature/journal/v432/n7018/full/nature0...

[2] - http://epublications.bond.edu.au/cgi/viewcontent.cgi?article...

Hello? Frog DNA. Duh! :)

Just keep a tight grip on lysine and everything will work out :)

That's exactly how the DNA sequencing works for fresh samples. https://en.m.wikipedia.org/wiki/Sequence_assembly We don't have the technology to do more than a few thousand bases in one go at the moment, so all modern sequencing means chopping up the sample, analysis, and then statistics based reassembly.

I don't know how it relates to million years old samples though. Maybe someone else knows why that's not easily applicable. I'd guess degradation being pretty random leaves chunks which are too small for analysis. (pure speculation, please educate me)

"For more than 7,000 hours over the past five years, Mitchell has slowly exposed the fossil’s skin and bone. The painstaking process is like freeing compressed talcum powder from concrete. “You almost have to fight for every millimeter,” he says."

Wow! I had no idea this took so long.

Archaeologists are heroes. They spend years painstakingly restoring things. Many of the digs also take many years of tedious work.

I just wish they got more recognition for their work. They do hard things over long periods of time and barely get a headline... which is good that their finds aren't oversensationalized, but, I think they themselves need more direct acknowledgement.

That's a big problem in society these days. People who do solid work in the background get no recognition. Science can't work if nobody is willing to produce the data other people can work with.

Alternatively, we could figure out how to automate his job away.

That's exactly the point. If you can figure out how to automate the job come back with a solution. But until then give them respect. They do difficult that can't be automated so far.

Depends. We already automated big parts of the job that we could.

To give a stupid example I came up with in five seconds: nobody needs to draw pictures of finds anymore, we can just use cameras.

Yes, the parts that can be automated now are already automated. But the parts that are left are hard to automate and not glamorous.

I met a guy who used to work for the forest service around where I live. His job was to head to surveyed forestry sites (i.e. potential future logging camps and what not) and draw pictures of all the archaeological artifacts. He was eventually replaced by a camera.

I went to a talk about dinosaurs once. Apparently you can volunteer for digs. But you have to work your way up if you want to work on fossils.

Does anyone have any experience with this and what it entails?

They both do digging and restoring, but only paleontologists study dinosaurs.

In this case, we got lucky that the skin was fossilized enough to be durable enough to be exposed (with a lot of care I'm sure). But I wonder how much fossil data in the loose surrounding soil is lost being swept away in the standard process of getting to the bones. For example, if one could apply a 3D scanner/sensor which could pick out density/composition around the bones before they were removed from the earth, what forms would we then be able to see...

Most things that die are quickly picked clean to the bones by scavengers, insects, etc. I doubt for a normal skeleton there's much left around it.

But cases where that information is preserved are probably more prevalent that this case where the soft tissue was fossilized by harder minerals.

So I would guess in terms of probability of occurence: skin-hard-fossilized < soft-tissue-soft "fossilized" < picked clean...

Jesus. I had to convert to weeks to get an idea and it's 5 years of about 27 hours a week, and that's just the average.

Back in 2005, researchers found soft tissues in a T-rex fossil (hollow blood vessels retaining their original flexibility, elasticity, and resilience): http://www.rpgroup.caltech.edu/~natsirt/stuff/Schweitzer%20S... IIRC they were cutting the large fossil to transport it, and it is while cutting it that they unexpectedly stumbled upon these soft tissues inside. This discovery was so mind-boggling at the time.

What research has been conducted on this specific 2005 T-rex specimen? The scientific community seemed ecstatic after finding it, but I do not remember any significant discovery made from the tissue.

>Researchers suspect it initially fossilized whole, but when it was found in 2011, only the front half, from the snout to the hips, was intact enough to recover.

Is this because of something that happened a long time ago, or because the mining machine ate the back end of the dinosaur? The article doesn't really make it clear.

Could anyone explain why being submerged in water would lead to particularly good fossilization? I would have thought it would do the exact opposite.

This is because silt can take the place of cells easily.

Because underwater there is less oxygen, less light and nice fine muddy floors.

It's only a matter of time until we stumble on an alien spacecraft buried in the rock.

Such an awesome article and photos, I want to see more photos!!!

But damn, reading the comments from creationists hurts :(

I was hoping there might be feathers preserved. Or is that not expected for this species?

Personally, I've not seen any evidence that ankylosaurs (including nodosaurs) had feathers. But who knows?

Can we use some of the skin and soft tissue to recreate the dinosaur using CRISPR?

I believe the issue is that DNAs half life is short (521 years in bone[1]) so after 110 million years, the DNA is pretty degraded.

1. http://www.the-scientist.com/?articles.view/articleNo/32799/...

Is it possible to use deep learning to fill out the missing parts? I am guessing that DNA is like code with a set of instructions encoded.

You could always fill in the gaps with amphibian DNA.

I imagine that is a Jurassic Park reference and not an actual suggestion. However, if it is, you would just then end up with a frog.

You're right we should just build humanoid robots for the guests instead.

building either of those leads to violent ends.

> Is it possible to use deep learning to fill out the missing parts?

The half life is 521 years - there is nothing left to fill in. If you read the linked article you'll see even under perfect conditions all DNA is destroyed after about 6 million years. This fossil is 110 million years old.

If you use deep learning, the missing parts will be filled with something based on whatever you trained the model on. In other words, the training data won't be dinosaur DNA as we don't have that. At best, during training you can classify some DNA as "more dinosaur" and other DNA as "less dinosaur" and you hope the result will be some extrapolation towards "most dinosaur". Despite the practical limitations, it's certainly an interesting thought.

What if the training set is evolution data? To me CRISPR + Deep Learning seems like a powerful combination. Looking to see some amazing advances in this area.

Can we use CRISPR to create something from ~500 year old bones? Okay, I already know the answer.

There is no skin nor soft tissue, just fossilization of them.

Title needs correction: With FOSSILIZED skin and soft tissue.

Isn't that kind of obvious given that it is 110M years old or did you interpret this as potential dino-burger material?

Well, the headline says "intact".

Ok, we've de-intacted the title above.

Disagree.

Intact for a 110M year old fossil means just that, it does not mean that the tissue has not been fossilized, it means it has not decomposed as it normally would.

If soft tissue and skin follow their normal path all you'd have is bones. Intact here means that the material is still present, but in fossilized form (just like fossilized bones are no longer the same as real bones).

The 'intact' is very much important here because that means it is not just fragments.

But clearly many here understood it so that there is literally intact skin and tissues that could be used to extract DNA. So the word "intact" was misleading.

The context is archeology, not grocery shopping.

No, the context is _paleontology_. But I get your point. We disagree and I accept that.

Sometimes soft tissue does survive:

http://www.smithsonianmag.com/science-nature/dinosaur-shocke...

https://www.theverge.com/2015/6/9/8751897/dinosaur-cells-tis...

I think it's not fair to say that "soft tissue survives".

These stories are all about bone. When you look at a piece of fossilized dinosaur bone, it's all rock. What the first article (from 2006) discusses is the work of Mary Schweitzer who has published several papers claiming that she has been able to extract _proteins_ from the fossilized _bone_: specifically collagen. Others imagine seeing "red blood cell type of structures".

It's mainly one person, Mary Schweitzer, publishing these claims. Schweitzer's 2007 article with Asara was called into question e.g. by Pevzner et al. in 2008 and others.

The mineralization of bone may ofcourse leave imprints of microscopic tissue structures in the remaining rock. I wouldn't call it soft tissue surviving.

Let me offer a link with some quotes.

http://www.sandiegouniontribune.com/business/biotech/sdut-di...

"UC San Diego computational biologist Pavel Pevzner, a prominent skeptic, said the study doesn't change anything. Pevzner said these claims run up against a great body of research that has failed to find soft tissue components in much younger tissues. Moreover, he said previous criticism that one study's results were tainted by contamination has not been adequately addressed."

"One of the original claims made, that hemoglobin fragments purportedly from T. rex closely resembled those of ostriches, is likely the result of contamination with the lab's earlier work with ostriches, Pevzner said. No subsequent studies have ruled out that possibility.

"'The big elephant in the room of this research is actually an ostrich,' Pevzner said. 'There is no hemoglobin reported from much younger (fossil) samples, like cave bears, mastodons, or anything else. In samples 10,000 years old, you don't find hemoglobin. But they found hemoglobin ... It has become a textbook example of how science should not be made.'

Am I the only one getting Jurassic Park potential vibes off of this? The potential genetic information from this find is amazing.

Does any DNA survive that long? I thought I'd read somewhere that it gets destroyed relatively quickly.

Half life of 521 years.

At least add a link...

http://www.nature.com/news/dna-has-a-521-year-half-life-1.11...

From this article, it would appear that DNA would probably be unreadable at around the 1.5M year mark, well short of the 110M years that would be required to recover DNA from this dinosaur.

There was this, recently: http://www.sciencemag.org/news/2017/04/no-bones-no-problem-d...

That's only 50,000 years, though. Also, no idea what the quality of the DNA is at that point.

No it doesn't. Yet Neanderthal DNA has been sequenced.

In this case, "intact" means that the tissue was preserved in shape long enough for the sample to fossilize. Not that it actually survived in original chemical composition for 100 million years.

My god look at the 'armor' on that thing. Humans are weak! But we can also build bazookas. Thank you asteroid, I would not be here today moving electrons to this server.

edit: does rapid-under sea burial mean it drowned? haha

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