Discovering the Colors of Fossil Creatures

Until recently, the colors of ancient life forms existed only in our imaginations. In museums and on the big screen, we have seen fossil creatures portrayed in striking colors, but those reconstructions were based on very little scientific evidence. However, over the past decade or so, new fossil discoveries and new technologies have given us the chemical evidence needed to work out the actual pigmentation of long-dead organisms. X-ray imaging, which can detect minute traces of the original pigments, has played an important role in that story. This lecture will explore that new area of scientific study, including discoveries made with advanced X-ray imaging techniques at SLAC.



hi and welcome to this installment of the slap public lecture series I'm doctor Nick Edwards and I'm a research

associate at SLAC National Accelerator Laboratory for this lecture I'm going to tell you about how my colleagues and I

have used the intense x-rays generated by particle accelerator slack's Stanford synchrotron radiation

light source to study fossils and discover the colors of ancient creatures

now I already mention quite a few big words there don't worry I will go through everything you need to know if

you still have questions at the end of this or maybe want to know more about a particular topic I discuss join us for

the live Q&A zoom session on the 2nd of June at 7:30 Pacific time the details

are on the slack public lecture website we're going to be joined by Hoover Bergeron who is our group's resident

physicist at SLAC Roy regalia our lead geochemist from the University of Manchester in the UK and Jennifer ohne

the lead paleontologist at the Children's Museum of Indianapolis we also do research other than discovering

the color of fossil creatures so if you'd like to hear more about that then zoom in if you're watching this after

June 2nd don't worry the Q&A session will be posted online and maybe your question was covered so what to expect

from this lecture ultimately I'm going to talk about how over the last 13 years or so my colleagues and I have

essentially tried to understand what fossils are made of so it's a commonly held view that fossils are just dusty

lumps of rock like this ammonites and skeletons and museums that essentially

just tell us about the shape of extinct organisms now there is a lot of paleontologists can decipher from these

fossils for example they can give us ideas about how an animal moved by seeing how the bones fit together and we

can interpret evolutionary relationships by tracking the changes in the shapes of Bones and other tissues through time and

we can interpret things pretty obviously like diet from things like the shape of teeth but ultimately all matter being a

human a cat or something non-biological like rocks or metal are made up of atoms

of elements a raisin or an almost infinite number of ways how different atoms combine together to different

materials defines their properties and they behave now a biological system like a human is just a big bag of wet

chemistry and you've probably been heard us pork head has been described that being carbon-based that's because we're

mostly made up of the element carbon you also pay familiar with iron that's in your blood or calcium in your bones but

you may not realize that we also have a lot of other chemical elements like copper zinc and manganese and many more

that are integral to many of the molecules that made you molecules like those that make your hair eyes or

skin a certain color it is this chemistry that I and my colleagues are

interested in because if we can identify elements in specific parts of a fossil that came from the once living organisms

we may be able to gain new insight into how this actually animal actually functioned at a biochemical level now

the holy grail of this biochemistry is DNA the blueprint for an organism unfortunately DNA degree is very rapidly once an organism dies and we're not going to be talking about it here we're going to be talking about how

about trying to identify elements and fossils that may indicate the presence of certain biochemical processes and in

this lecture we are going to focus on those elements associated with color now you may not realize that until recently

we didn't actually know color the color of extinct life forms were despite what

you may have seen in movies or on TV there is very little direct so much scientific evidence for color in the

fossil record this for example is technically as valid as any other color

reconstruction and we're interested because color is very important to life in general and defines many of the ways

that an animal animal behaves such as being camouflaged or being brightly

colored to attract a mate pretty important behavioral characteristics so you can understand

how paleontologists would be interested in these details but before we go into that for the first part of this lecture

I'm going to talk about how we can uncover this information and in this case the way we obtained the data we

need is just as cool as the data itself and I think it is important that we take some time to cover that subject so first

a little bit about me how does a little boy dinosaurs from England end up working at

a particle accelerator in California well as you can see I like dinosaurs

ever since I was a little kid and I always wanted to be a paleontologist so I had lots of other interests at school

and as I grew up but my interest for dinosaurs and paleontology never really went away so I decided to pursue that as

a career now there aren't really any degrees in paleontology exactly but there are degrees in geology where you

can specialize in paleontology so that's what I did I went to raw Holloway University of London not just not too

far outside of London and I graduated there in 2006 and then I decided I still

like rocks and fossils so I decided to go off and do a PhD and luckily I was

taken on to do a PhD in paleontology at the University of Manchester which I started in 2007 and it was in the winter

of 2007 that I first came across slack a synchrotron and the joy of x-rays so we

were invited by some colleagues of my PhD advisors to go visit them seeing what they were doing with doing some

cool things with fossils at the synchrotron and we were hooked immediately the data that they were

collecting looked amazing we could really see some awesome potential for what the data was telling us about these

fossils and it was just super cool it's a big science machine beep facility really cool big science and so what they

were actually doing was using a technique developed by a slack scientist

called mover Bergman who is joining us for the Q&A where he had developed a

rapid x-ray fluorescence imaging technique now I'll go into x-ray fluorescence imaging later so don't

worry about it but basically it's the ability to image the chemistry of a large object by large

I mean bigger than like a one square centimeter or half an inch or something like that whatever the

conversion is but a centimeter and real unit and what he did was look at some

ancient manuscripts that revealed hidden writings underneath by being able to

look at the chemistry below images covered over the top and in this case

this was the Archimedes palimpsest we don't have time to talk about this but this kind of gives a general idea and so

those colleagues who invited us over had heard about the Bowman's work looking

ancient manuscripts and thought hey this would be really cool with fossils and then we came along as well and so a bit

of serendipity there and yeah kind of a bit stumbled on it by chance but anyway

super cool and we realized what the potential of this could be I ended up finishing my PhD at Manchester in 2012

and through some of the results that we gained during those years while I was

doing my PhD and there's a research group in general I'll talk about one of those papers later but based on the

success of that research we got a grant to fund me as a postdoctoral research associate at Manchester and I stayed at

master for another four years continuing this work on do it using the synchrotron

to study fossils and investigate color and then finally after four years of the

postdoc an opportunity came up for me to move to California and join slack to

work on the x-ray fluorescence imaging beam lights and this was a dream country because I always this was the most

bender bit I enjoyed most about coming to the synchrotron was doing the experiment and all the experience I've

gained over there kind of helped lay the foundation for what would become a

career in synchrotron sciences but

before we start talking about specific fossils and their color I think it's really beneficial that we first cover

how we actually collect the data using x-rays specifically those produced by a

synchrotron and because the way we collect the data is just as cool as the data itself so

first water x-rays x-rays are electromagnetic radiation just like

visible light radio waves and microwaves among others you may have heard of and all of these radiation travels as waves

now the electromagnetic spectrum is the range of frequencies and their

respective wavelengths and photon energies now wavelengths can range from thousands of kilometers all the way down

to the nucleus of an atom now the electromagnetic waves of each of these bands have different

characteristics such as how they interact with matter and their practical applications now we want to use x-rays

because they have high enough energy to ionize atoms and I'll get into that when we start to talk about x-ray

fluorescence in a little bit but you'll be familiar with hospital x-rays and that's because they have high enough

energy to pass through fleshy bits but not bone which is why we see a contrast

on an x-ray film but we need to generate

these x-rays and we need to generate lots of x-rays and we need to generate

x-rays in a very controlled way so we can manipulate them make them do what we want and the way we do that is to use a

synchrotron now this is where really

modern-day physics meets ancient world fossils now a synchrotron is a particle

accelerator and SS RL was one of the first synchrotrons a lot of the research

we do we have also done at Diamond light source in the UK but basically a particle accelerator accelerates

particles too near the speed of light using huge electromagnets and that's an insane speed that's about as fast as

anything can go as far as we understand it here we are inside the ring at s srl

and again idea to the sort of scale of the engineering they're involved in a

particle accelerator so the cistrome was originally designed as a particle smasher that is sending particles in

opposite directions those electromagnets and smashing them into each other in order to study

subatomic particles but when these particles were accelerated at such

insane speeds in Anisa in a circular path it was found that there was huge

amounts of radiation being emitted out the side and this was kind of a pain because we didn't want this radiation I

had to be shielded against and that kind of was it for a little while but then

some clever people realized that this radiation was could be very useful for

performing a wide range of experiments and so sometimes people found out that

realized that if you could punch a hole in the side of the synchrotron and let some of this radiation out and then

control it with different optics and different mechanical components you could actually channel it and control it

to do the things we want and this is what's called a beam line and a

synchrotron now and lots of synchrotron is being built today are pretty much dedicated to generating synchrotron

radiation as well as doing some particle smashing work now there are many of

these beam lines around a synchrotron and they're so Sharelle has over 20 of

these beam lines with many substations in there as well and research using the

synchrotron ssro covers a wide range of disciplines such as the energy sciences looking at battery technology biomedical

science environmental science and the

one little bit that we do down here is our x-ray fluorescence imaging of things like fossils and ancient artifacts here

we are inside s srl itself and here we are inside some of the experimental

hutches where the x-rays come out and say this is one of the x-ray

fluorescence imaging stations where we try to understand the chemistry of ancient artifacts so I've mentioned

their x-rays and x-ray fluorescence imaging so exactly what is x-ray fluorescence imaging now I mentioned the

ionization of earlier when we talked about the electromagnetic spectrum and x-rays and

I'm going to go into that now so without getting into too much detail like the

haze both as a wave and a particle and that particle is called a photon ie one

unit of light and that's what we've got here represented in this little red dot and represents one x-ray particle coming

out of the signature and now we have here kind of like a stylized cartoon atom which you may or may not be

familiar with but an atom just to recap is the building blocks of all matter and

with an each atom is an element essentially but the difference between

the elements is their atomic configuration actually so an atom consists of protons and neutrons in its

nucleus and electrons orbiting around the outside now it's actually kind of like a little cloud of electrons but

this is the best way to represent it in two-dimensional space and the different configuration and number of protons

neutrons and electrons determines what an element is so iron has different

protons neutrons and electrons to calcium for example and we'll show how that's useful in a second but what we're

going to do is iron eyes this app and we're going to bother it we're going to make it unstable using the x-rays from

the synchrotron so and this is really useful process because we use this to be

able to identify elements and so here comes our single x-ray photon of which

there are millions and billions coming out any time that this is just one representing one of them it comes in and

it's high enough energy to knock an electron out of inner shell of the atom

this is self is called the photoelectric effect and if I say now that state here

is the atom being ionized now the atom wants to restabilized itself and it does

that by filling that hole we just created with an electron from one of the

higher orbitals like so what's really cool about this is is that

change in electron falling from 1 to a 1 orbital to another that generates a brand new x-ray which we call the full

arrest x-ray now what's really interesting about that is that that

x-ray has a wavelength or a photon energy that is characteristic to the

atom that it came from and we detect these x-rays and by able to detect the

wavelength or the energy of this x-ray that means we're able to identify the atom of that x-ray came from now when

we're bombarding our sample with lots of x-rays from the synchrotron we're exciting lots of different atoms at the

same time so we get lots of different fluoresced x-rays coming out of our sample of different wavelengths and

energies so how can we differentiate between them so on the right here is

what we typically get out of a synchrotron called an x-ray fluorescence spectrum that's when we just have our

actuary detector pointing at our sample while being bombarded by x-rays and

where it's able to detect the different energy of those different x-ray photons

and separate them out into air so that we can see them in this spectrum and

what we have here is the photon energy across the bottom and how many the x-ray detector has detected up the vertical

side there and so what we get is wiggly lines like this that show us how much of

each x-ray we've detected and so for example we have in this spectrum we have

lots of photons that have an energy of about 3,700 electron volts and that is

the energy of photons emitting from a calcium from calcium atoms and at 6,400

evie roughly we have lots of photons coming from iron atoms among lots of

other different elements there now as I said lots of different x-rays of different wavelengths and energies are

being emitted from our sample while we're hitting it with synchrotron x-rays and so and this is represented here by

this kind of bitte warten fine line diagram of the electron orbitals I talked about where

one force from a higher one to a lower one now we label these as these letters here

so K shell L gel M shell and shell and it's actually the transition between

these different shells that generates different energies of photons coming out

so in this spectrum here we're looking mostly at what we are calling K alpha

and K beta and simply that represents electrons that are falling from the L lines down to the K line here that's the

K alpha that's one of the most dominant peak we usually see in an x-ray fluorescence spectrum the next one we

commonly get is what's called a K beta and that falls from a n line down to the

K line and that's why we call in case else cuz these fall to the K shell there's also lots of other lines that we

don't that we're not seeing in this spectrum but a lot of research is done on as well excuse me Kitty which is the

an M & M electron shell M shell electron falling to L shell so those are called L

lines and then finally end to M so hopefully that's a good actor you can

understand the significance and importance of that sort of atomic

process going on in our samples and how we can use that to identify elements now

that's great we can put the synchrotron beam like on our sample and we essentially get an inventory of what

elements are present that's great and can be done in lots of other different types of instruments as well and both be

really cool and what's really interesting for us is whether we can hatch that we really want to know what

are elements or inventory is for different parts of our sample not just under four different parts of our sample

not just under one particular spot now we could just drive around rounding on different spots and collecting a

spectrum like this but that's not very useful and is actually quite could be quite time-consuming so what's

been did what has been developed and is pretty common for the different techniques but I'll get into why the

synchrotron is particularly good at this in the second is x-ray fluorescence imaging now all that is is that we have

the same synchrotron beam the same process is happening here but what we do

instead is we move the sample backwards and forwards in front of the beam so here's a little cartoony animation of

representing our x-ray beam coming from the synchrotron and our 4xs rays coming

out into a detector and we're moving our sample backwards and forwards and if we time our stage movement and our computer

data collection properly we are able to build up the chemical image pixel by

pixel line by line and then we're able to see essentially a picture of where

the different elements are here is the same here is a representation of the

animation here so here we see a fossil going backwards and forwards now you can't see the x-ray beam it's not like

cool lasers or anything but there is an x-ray beam coming through here and here is our x-ray detector and here is our

fossil moving backwards and forwards and as it moves backwards and forwards we start to see the data come through live

line by line so why use a synchrotron

well the synchrotron has many really awesome advantages compared to other techniques which can also generate x-ray

images with this kind of process the first thing is is that the synchrotron

Geraint generates lots of x-rays much more x-rays than other instruments

generate in their beams to excite their atoms and that makes us much more

sensitive to elements that in lower concentrations now that's really important to us in looking at biological

systems because often elements are in very tiny quantities but significant quantities and quite simply the more

input there is the more output there is so statistically we're much more likely to hit an atom that is in low

concentrations with a lot of x-rays than we are with only a few x-rays and

the other advantage of having lots of x-rays means we don't have to sit on one spot for a long time to get a good

signal so we can scan faster which means we can scan bigger things in a shorter amount of time and that's really good

for fossils in particular another good thing for things like cultural and natural heritage artifacts such as

fossils is the fact that we can actually work in what's called ambient conditions that is we can essentially work in room

temperature and normal atmospheric pressures unlike other techniques like

scanning electron microscopes which require a vacuum chamber and that's very important because a lot of

paleontologists don't want us mashing up their samples into small bits in order

to go do a bit of chemical analysis some fossils extremely rare and precious or they might sometimes is even only one of

them so in order to do chemical analysis on a lot of fossils you just couldn't do

it um it wouldn't be allowed so being able to put in a fossil untouched and

unmolested into the x-ray beam very useful and it's also very flattened

because of that it's also very flexible in sample size and shape fossils don't conform to nice perfect samples that a

lot of techniques require so we can put in a big lumpy piece of rock with a

fossil in it and the synchrotron handles it just fine and finally while most it the final

important thing is that essentially this technique is non-destructive unlike other techniques where as I said where

you have to smash things to pieces and coat them in things in order to look at them the synchrotron doesn't require

that we put the sample in we scan it we take it out and it looks just like it

did before we did the analysis and a lot of other analytical techniques actually destroy the sample during the analysis

so it's gone forever so a lot of really good advantages there to using the

singer trough now I'm not going to delve into this part too quickly but it is really important because actually the

way that we're able to manipulate x-rays at synchrotron beamlines means we can do

performance an analysis called x-ray absorption now I'm not going to get into

much detail here because there's no time but essentially what we do is we put our

beam on our sample and we essentially generate a wiggly line

I thought all quarters x-ray absorption spectrum now say don't don't worry all stop getting too too overwhelmed by this

but the main take-home point from this is is that the shape of these wiggly lines helps us identify the chemistry

around an atom that we're interested in so for example you may not know or may

not realize that each element depending on how its bound in terms of its

arrangement of atoms to other elements generates different compounds and a

really good example is iron so you have iron metal Fe but we're probably all

familiar with the fact that you can iron rust and what is rust rust is iron with

oxygens around it as we can and here is an x-ray absorption spectrum of iron

rust on the left and has them where we collect an x-ray absorption spectrum the

spectrum has a very specifically shaped wiggly line now another type of iron is

pyrite or fool's gold and that's iron an iron atoms surrounded by a couple of

Sulphurs same element very different properties and characteristics one is

rusty Brown and we see it all the time pyrite almost looks like a gold color

and as you can see the wiggly line here is very different to the rust so x-ray

absorption is extremely useful and you'll see why that's significant when we look at fossils and looking at the

elements that we're interested in because some elements are inorganic some

are organic and come from different places are surrounded by different elements and so when we're doing our

chemical imaging of our fossils we want to know are those element

is organic or inorganic what are they just knowing that it's copper or iron or nickel or whatever isn't enough we need

to know what's surrounding them what compound is it essentially and that's

important because we need to try and say with a reasonable degree of certainty whether the elements that we're seeing

in our fossils have come from the external environment which is likely after tens of hundreds of millions of

years or is it has it come from the organism itself and hopefully we'll be

able to tell the difference between the two by being able to perform this experiment and see their different

atomic arrangements so not too much detail hopefully but important

nonetheless that we do cover the basics there now on to some data

thanks for bass hopefully you've stuck with us for this long and now I'll actually get into looking at some fossils

okay so we've we're done we're done with the background stuff synchrotrons x-rays

x-ray fluorescence imaging hopefully that was interesting enough and you're still here

but now we're here we're going to see how the synchrotron has generated some really cool data and we're actually

going to go through a little bit of a chronological narrative here about how the research developed over the years of

using the synchrotron because we kind of didn't know what the synchrotron would tell us in the early day so we kind of

started like with the advert as the advantages I mentioned earlier that we could look at fossils that couldn't have

chemical analysis done before and so we put in lots of cool fossils and kind of

followed the data we just wanted to see what the data showed we really had no idea what we were going to find and one

of the actual driving thoughts that we had that the synchrotron could tell us was that we might be able to find things

that we don't chemical ghosts what do I mean by that well I mean is there hidden

hidden chemistry in the fossils that we can't see with the naked eye that might

tell us something about the original animal that we didn't know before for example is there remnant chemistry

soft tissues which we can't see anymore with the naked eye such as feathers skin

fur things like that and long story short the answer is yes and we one of

our first discoveries using synchrotron x-ray data did exactly that and we even

and even better we did on one of the coolest most well-known and important fossils ever discovered this is

Archaeopteryx Archaeopteryx you may or may not know has been dubbed one of the

world's first missing links between dinosaurs and birds now things have

changed a little bit in the last few years about how about evolutionary ideas between dinosaurs and birds but really

important scientifically and culturally scientifically because for intents and

purposes Archaeopteryx looks like a dinosaur a little dinosaur running around a lagoon area in Germany 150

million years ago in the Jurassic period if you were to just look at its skeleton it looks like a little dinosaur about

the size of a chicken as I said it has teeth in its mouth claws on its hands

and a long bony tail so that's a

dinosaur bio-intensive person actually if you put this skeleton of Archaeopteryx next to another species of

dinosaur called Compsognathus you'd better be able to tell the difference so what is the difference well the stunning

discovery when these first specimens were discovered back in the 1800s was

feather impressions surrounding the animal surrounding the end attached to

the skeleton now it was a bit hard to see in that optical image but essentially what you could see is things

that looks like feathers as though they'd be squished into the rock but now the soft tissues of the feathers aren't

there anymore they're just gone away it's literally like somebody pressed a feather into some clay and took it away now this was a revelation because when

were first discovered they there was no indication or any idea that birds and dinosaurs might be related and from the

cultural point of view I mentioned this is around the time when Darwin had

published his first edition on the Origin of Species where he suggested that species transition from one species

into another but one of the main criticisms of his work was that if this if this process happened the process of

evolution we should see these transitional species in the fossil

record and up to that point nobody had discovered any and not long after his

first editions one of the first complete nearly complete Archaeopteryx specimens

was found showing exactly this the two seemingly disparate features of the

dinosaur skeleton but feathers which is the definition of a bird attached to one

another so really important from a cultural and scientific and pain it's a

logical view right there and they're only actually believed 14 of these in

the world this sample is number 12 anyway so this is actually number 12 and

we actually studied the first one is well called the holotype which I'll get to later and also the so another one

early one as well and so this specimen

as you can imagine has been extremely well studied paleontologists did what they normally do and looked at the shape

of the bones and the feathers and try to make evolutionary two interpretations from looking at it under visible light

and sometimes some people looked altra Beiler and other wavelengths - but nobody looked at the chemistry of this

and to all intents and purposes people had just said well these feathers are simply impressions there's nothing left

there that's all we can tell is we can look at the impressions in the rock and that's all we can tell now we thought

this was a prime example for the synchrotron it's rare there's only 12 or 40 at there's only 14 of them and

there's potentially some chemistry there because we there's some indication of soft tissues

plus iconic specimen really of white interest and the results didn't

disappoint here is the key image from that work which is the element phosphorus now

phosphorus is as you may know is part of your bones bones a calcium phosphate

mostly and that means they're mostly made up of calcium and phosphorus so

it's no surprise to see that phosphorus is highly concentrated here in lighter white colors compared to less in the

dark in the bones but what was a really nice surprise was that we can actually

see the central shaft of the feathers in phosphorus and we can see them here and

here I'll zoom in in a second but this

is the key to doing this large x-ray fluorescence imaging because the end of

sensitivity and also testaments of sensitivity in the synchrotron because these are extremely faint signals that

we're looking at here and these are signals that we can only really tell are

there because we see them and interpret them with our own eyes as following structures we see in the visible light

other techniques if we had to chip a bit off or put them in another x-ray source

which could only scan a centimeter at a time we'd have had to be very selective out where we picked and we may have

missed this feature completely but being able to scan the whole thing means we're able to see correlations between the

feathers and the chemistry and this was a really big result and what's more

phosphorus is actually an element that we exceed in modern feathers so here we

are zoomed in area you can see some of the lineage here a bit better hopefully and the same on the other side so that

was a really stunning result and that was published back in 2010 really showed what the power of the synchrotron could

do now it wasn't just phosphorus that we

were looking at we were looking at at different elements all at the same time - and I mentioned earlier about

different elements coming from different places and we want to be able to tell the difference now here's a note here's

the element manganese which is very common in rocks and actually very common in fluids that move around in rocks and

they actually form very distinctive precipitate or crystalline structures

and we see that on the bones of the Archaeopteryx here and they make these a

little firm pretty firm patterns now if we have just taken the x-ray daemon plunked it on those areas that are in

white there we would have seen a manganese peak and we may have interpreted that as belonging to

Archaeopteryx because manganese is also an important element inside organisms as

well not only into chemical fluids but because we can image it on this scale we can see the characteristic patterns that

make up this inorganic process and interpret that as not being associated

with the animal not only that we have

curatorial artifacts so more recent

things where people have come along and try to pretty up specimens and can

actually see here where we have modern filler filling in holes of the bones and

then finally this is a favorite of mine in chlorine we can actually see

fingerprints around the outside of the specimen where our sweaty paleontologists have been manhandling

this specimen and this is kind of well funny but it's also important because

clearly we have contamination there so somebody was to come along and do some organic analyses and choose that area it

would very likely be contaminated so very useful in a screening tool sense as

well so now we hike in ewwww

hello so now we move on to colorful chemistry and investigating how we can detect

colors like on my pretty little kitty here in the fossil record and so we move

on to our next key publication using the synchrotron x-rays and where we first

kind of get the idea that we may have elements present in fossils that can

tell us about specific biological processes in this case color so we

actually this was a surprise result to us as well this was another beautiful fossil that we were able to get access

to and scan again kind of rare seeing lots of this is a bird from China a bit

later than Archaeopteryx now in the Cretaceous period about 30 million years

later and again an ideal candidate for the synchrotron because it's precious a

little bit rare very delicate and because it preserved beautifully

beautifully preserved feathers all around the outside though you can see here in this kind of dark dark black

carbon area and a lot of people thought that this exceptional preservation kind

of only extended to the microscopic level at most this isn't quite one of those but this is what the time was

considered one of the first true birds in that it had a beak with no teeth and

made out of keratin like the fingernail material that we have so we'll talk

about keratin a bit later as well so keep that in mind so we scanned it

with the synchrotron on the right here is a false color image so higher intensity of these colors means there's

more of it and this is actually kind of just to represent the distribution

doesn't really represent true levels but the thing here is is that zinc is represented in green and that's kind of

there to show the background level or background of the rock that it's encased in blue um is where the calcium is and

again like we saw on the Archaeopteryx before with the phosphorus cows is concentrated within the bones not

surprising because bones are calcium phosphate as I said so no surprise that but what was a real surprise was to see

copper colored here in red now this is in the colors that the synchrotron

generates these are colors that we make up afterwards to help us see the difference between the elements a copper

x-ray is not really red and a zinc extra is already green these are just colors that we use to try and illustrate the

distributions in elements so this result that we see in copper being highly

concentrated to the feathers was a bit of a surprise and so we wanted to understand where that copper may have

come from now as scientists we often

study the present to understand the past and that's particularly true paleontology so what we decided to do

was dig into the literature and see if there's any reason for copper to be in

feathers we then looked to modern-day organisms that we looked at some

feathers here's a couple here but draw your attention to the main one which is panel II here which believe is blue jay

feather and we like this because it was darkly pigmented and then had a white tip in a very sharp transition and all

three colors of that transition between pigmented and unpigmented was reflected

in the copper map so that kind of gave us a first indication that the copper

that we see in our fossil might be related to the pigment distribution so

we dug into the literature as well after find it and doing this imaging getting this imaging data and we found that

indeed copper is present in feathers and it's usually present in feathers because

of the presence of a certain type of pigment called melanin and melanin is

actually pretty ubiquitous in life it's the same pigment that pigments is pigments mine and your hair skin is the

reason why you tan and it's present because the melanin molecule likes to

stick to metals the atoms of metals such as copper zinc and calcium and we'll get

more into that later and actually a lot of studies on melanin look at squid ink because squid

ink is a particular type of melanin called you melanin and we'll get to that in a second as well so we decided to look at

a fossil and modern squid and we could actually see high concentrations of copper in their ink sac so we started to

formulate an idea that the presence of copper may indicate the presence of a

particular type of melanin pigment called you melanin so we went the next

step further because what we wanted to do we wanted to get a bit more confident is to wear this copper came from but

it's quite possible that the copper in the fossil of the bird itself could have been sucked up from the outside while

the animal was degrading so or it could have been brought in by some other

secondary process so we did the absorption expect vector osku P on the copper they explained earlier now what

was really cool about the results from that is that we found that the copper in the fossil was actually present as an

organic type structure that is a copper atom surrounded by oxygens or nitrogen

and so we wanted to know well does this copper kind of look like how it would

have looked in the melanin molecule so we reached out to a colleague and they

supplied us with their theoretical computational model for Melonie molecule so this is represented by all these

atomic balls around the outside here and what was really cool is that ah the

structure of our copper in our fossil fitted in the middle of our melanin

modern melanin computational model like a puzzle piece so this was another

really strong piece of evidence to us anyway that the copper we're seeing in the feathers of this 120 million year

old bird um actually came originally from a pigment molecule eumelanin and in

that sense that the copper image actually represented the distribution of

that pigment in the organism when it was alive and so we postulated this reconstruction

of the dark hue melanin pigment we thought it would be present where we saw

the highest intensities of copper and not present where we saw low intensities of copper in particular out here on the

very end feathers of the wings which you could see clearly in the original fossil down here but is not present in copper

over there and so we also believe that I mentioned in the introduction that

colors in that we see on ancient organisms are completely made up there's not much direct scientific evidence for

that so this was we believed one of the first times that a pigment

reconstruction had been made based on direct scientific data not only that that from covering a whole organism

instead of a few spots and being extrapolated out and this was published in science one of the top scientific

journals back in 2012 so that was our really cool second

huge result and that spawned actually my

postdoc and another three years of funded research to specifically look for pigment in the fossil record I don't

have time to go into all the suits today but I'll take the key ones out of here and so that led us on to studying

pigments in a lot more detail and particularly melanin now why look at

melanin in particular there are actually lots of different pigments out there

that make lots of different colors so for example melanin which I'll get into

a minute is responsible for a couple of different hues but then there's also things like carotenoids which are

present in things like that create bright blues reds Pink's things like that and particularly those you've been

familiar with those in flamingos and but in the in my cat here it's likely that

she's mostly made God using melanin for her pigment so and the other key thing

about melanin too is that actually melanin is the only pigment that really associates with metals metal atoms in

particular as opposed to the others which are what we would say a purely organic compounds

so really melanin is pretty conducive to being studied at the synchrotron because it has a metal element component such as

this which the synchrotron is able to detect so what is melanin well melanin

is actually kind of hard to characterize it's a very messy molecule made up of lots of subsections as I said there's

two forms of eumelanin there are two forms of melanin eumelanin which part of

our structures illustrated on the light right here don't this is a kind of a typical organic e looking molecule of

carbon rings with oxygens and hydrogen scattered around them and nitrogen and

so eumelanin on the left there is mainly

those elements i just mentioned and responsible for sort of dark brown black type colors and the other type of

melanin is what's called FeO melanin and fire melanin is responsible for the

reddish blond huge that we see in people's blonde hair and red-headed

people in particular it's very rich in fair melanin now we were looking at

trying to understand which elements are associated with which type of melanin so

we could get an idea because often when melanin is present it tends to dominate a pigment of a tissue and as we saw in

see Sanctus it seemed that like copper had a particularly high affinity for you

melanin you melanin has lots of these kind of open-ended parts of the molecule which really good to sticking and

grabbing up different elements and that actually makes and say with the fair

melanin to actually with these end members all these ligands sticking out the side that makes it a very versatile

molecule because as I said it's something that it's actually pigment that's present when we tan we create more melanin as we tagged and that's

because it's a UV protector so and then not only that its present as

a pigment in our hair eyes skin whatever so for animals anyway it's a big a big

part in how they produce color patterns in their in their external tissues being

used in either mating rituals or for camouflage for example so from a fossil

paleontology point of view being able to identify these elements and map their distribution and fossils is kind of

important and interesting so we went out and tackled a couple of different things

now the main thing to pick out between these two molecules here is that if

there is essentially not much difference in their overall structure I mean they look different shape but that's not

something we can tell with the synchrotron the results we were able to pick here and we'll talk about later so

Fenton there's sulfur present in AML and into and we'll get it when there's no sovereign eumelanin and we'll get on to

that a bit later when we look at modern feathers so here's the stew sulfur atoms

here in the structure and we'll get to that a bit later so I mentioned earlier

we'll we're back with Archaeopteryx now and we actually looked at the very first Archaeopteryx fossil which you think

well that's where doesn't look anything like the previous fossil I knew be right because the first Archaeopteryx fossil

was actually this single feather and importantly when this was discovered it pushed the back in the 1800s this was

actually pushed the origin of birds back into the Jurassic period as previously people thought they were after the

dinosaurs so pretty important fossil they're again only one of them in the world it's called the holotype which is

basically for any species there should be a holotype specimen of which all other fossils are compared to so

extremely precious but we were it because of the non destructive nature and the synchrotron we're able to take a look at its chemistry here it is being

scanned at the synchrotron back in 2012 or 2013 and we saw pretty similar

results to those in the fossil bird two computers Sanctus where we saw copper and nickel

present elements known to be associated with eumelanin and we also saw the presence of sulfur that we believed

capital was coming from the original sulfur present in the protein that

feathers are made out of keratin and so we saw more so along with other data we

collected and we saw we believe that we could create this pinguin reconstruction

of the feather showing a dark leading edge of the feather and a pale following

edge now the last sample we're going to

talk about after this modern feathers which is the fossil mouse was when we

started again inkling that we could try and identify fair melanin in the fossil record and try and differentiate between

the two pigments however we didn't have enough data to really justify our

conclusions in that paper I'm going to talk about on a fossil Mouse so we decided we needed to take a step

back and collect more data on modern melanin in order to understand what the

signals coming out of the synchrotron would be for modern tissues and so we decided to study melanin in a range of

modern birds so we took a look at feathers from for birds of prey all of

these birds were in rescue sanctuaries or rehabilitation centers so we didn't

go out bucking feathers off of wild birds these all-natural and bolted

naturally off of these birds and so what we have here on the left is a Harris Hawk and next to that we have a Kestrel

a barn owl and a red-tailed hawk and we picked these guys one because they're

relatively common birds of prey but they also had feathers with a variety of visibly anyway differently melon iced

feathers ranging from dark black all the way to a reddish hue Jerry Brown here in the bar now and not only that seeing

those different pigments in a single feather so we wanted to be getting rid of some ambiguity of seeing feathers

from different animals and different parts of the bird and literally go down to one feather so that's what we did we

looked at single feathers here are the optical images of the areas of those

feathers that we scanned so you can see nice clear differences in pigmentation there but we wanted to confirm what melanin was in there and in

fact did they even have melanin in there so we sent samples off to some colleagues in Japan who developed a

technique for quantifying melanin and indeed we got confirmation that the

different parts of the feathers with different levels of what to us looks like different pigment contain different

levels of melanin in particularly the Harris Hawk there you can see has a lot

of you melanin the dark black melanin in its dark area and a little bit of family

now that's okay because all most animals have a little bit of mix of the two even

even in what appears to be particularly black and particularly rare the Kestrel

next to it great comparison because we have a dark black stripe with a dark red area completely next to it and we saw

the right thing we saw that the black stripe has a lot of you melon bit of fur melanin the red area has a bit of you

melanin and a lot of fame Elenin the barn owl which seems to be much less

strong in pigmented and a lot less melanin overall but again the similar sort of ratios as we'd expect and then

finally the Harris Hawk here which is a very deep red mostly Pham Elenin with a

little bit a minute so we confirmed the presence of melanin in these feathers so

we scan them at the synchrotron t they are being scanned in the beam and here are some of the resulting images and so

we collect a lot of different notes but these are the key elements that are known or were known in the scientific

literature to be associated with melanin calcium zinc and copper with the optical down the right hand side and so what you

can see hopefully is that and what's pretty obvious to us anyway is that

these elements are stripped the presence of these elements in the feathers are strongly controlled by the presence of

the melanin Ament if they weren't we wouldn't see we would see different patterns in the

elements compared to what we see in the visible but actually we don't see that and especially in the Harris Hawk it's a

beautiful set of images here that we can see and the melanin concentration drops

off into the wide we get huge drops off in the element concentrations - we can

also see the stripes in the Kestrel and interestingly in that that's a little

different we don't see that strong copper signal that we saw before but

what we do see is the presence of calcium enriched in the dark stripes as

we see enriched in the black area in the Harris Hawk and then we actually see that there's more zinc in the red areas

of the Kestrel compared to its dark stripes so what and this actually matched what we saw in the literature -

to that fair melanin has a stronger affinity for zinc the new melanin does

so this kind of made a little bit of sense here here the other two feathers

following a very similar sort of pattern zinc associated with the red and calcium

associated with the dark and in fact it's only really when things are really strongly pigmented like the Harris Hawk

that we see tend to see copper concentrations detectable amounts so

more wiggly lines don't worry but the important thing here is that we have we

did work on the zinc work because we saw a difference in the zinc distributions

in these feathers and we also looked at so far as I mentioned earlier that fair melanin has sulfur in air could be a

defining characteristic here so looking at the zinc spectra first again these

wiggly lines the main thing to look out for is that the Harris Hawk here in black has this peak here and is quite a

nice symmetrical peak down here this kind of represents a zinc surrounded by oxygen the nitrogen and the same here

look as a natural eumelanin standard but what we see here in the Kestrel in

particular is that we get a secondary bump here on this peak and that's really

interesting because that represents the presence of sulfur so what we have there

in the zinc absorption spectra is a difference where we see a decent

contribution of zinc combate combined with sulfur as well as combined with oxygen nitrogen but we don't see the

sulfur at all in the very strongly you melon eyes version so that indicated to

us again and strengthens the idea that zinc has a very strong affinity to their melanin on the right here we actually

started looking at sulphur too because I mentioned sulfur was important in the structure for a melanin so what is the

difference or how does sulfur look in the molecule well these two molecules

here benzo thiazole benzo Phi Z both present in the family molecule and here

is their they use compounds extracted and we get very specific looking Wiggles and the other important wiggle that we

have here is oxidized glutathione otherwise known as a disulfide now this

represents the base protein the keratin that we have in our fingernails and in

the feathers because that two sulfur's joined together and that has a very distinct double peak here so we're

really interested in this double peak this benzo thighs are here and this

benzo fire zine so we looked at all the

feathers using the sulfur absorption spectroscopy and the key result here particularly from the Kestrel and the

red-tailed hawk is that we look at the white area which is kindly essentially

non-pigmented keratin protein so it should look like that oxidized glutathione we sue before the disulfide

and we see the characteristic double peak that we saw before next we looked

at the dark you melon eyes stripe of open and partly feminized strike for the

Kestrel and we see again dominated by the protein of the feather because that's what

to the sulfur in the feather is but we get some slightly different bumps here as well maybe that's indicative of some

fair melanin that we can detect but the real EQ is all here is the slight difference in this double peak here that

the fact that there's enough presence of fair melanin in the dark red area that

the signal from this petite type of sulfur molecule is actually changing the

shape of the spectra and we see that as this peak being higher than this peak so

what we're actually able to show here is that when we looked at the sulfur we saw a difference in the wiggly lines and

when we looked at the zinc we saw a different in the wiggly lines both important because it's the presence of

the added sulfur from the fair millennion molecule in the heavily red areas of the feather so this was really

cool we had this data and we were armed with it we thought we had a good way to

conclusively or pretty strongly look at FeO melanin and be able to take man in

fossils and so we move on to our final fossil which was only published last

year this is a fossil mouse called epidemis basically it's an extinct it's

an extinct species of a one mouse like today's field mouse and beautifully

preserved software you can see it's pretty tiny only one centimeter scale bar there so only yay big and this was

found in Germany again villa housing the location is called which consisted of a

very small deep lake which didn't have any oxygen to the bottom so it's pretty

conducive to preserving soft tissues in an exceptional way and you can see that

here because we can always see the individual hairs and of the fur surrounding this animal and we had

scanned this at the synchrotron a few years before we even undertook the feather study but now that we were armed

with that feather melanin data we were able to although this mouse again and in fact

here's the false color image and again we see the phosphorus here which is colored blue concentrations of bones as

we saw it makes sense before the red represents an organic salt fortune I didn't have time to go into how we map

organic sulfur specifically but that shows up in the fur beautifully and

actually just going back to the phosphorus you can even see its little ear lobes which makes sense because we've got phosphorus in the collagen of

our ears and then finally with the this area is dominated by yellow it's

actually a mix of the presence of zinc which is colored in green and the organic sulfur so we actually have a mix

of zinc and sulfur in these areas kind of in the fur and skin areas like this

and again hopefully I've emphasized that the stereotype of paleontology being a

science dominated by people in tweed jacket and elbow patches or being Ross

from friends isn't true we are scientists like all others and using

state-of-the-art techniques to try and understand more about the ancient world I've talked a lot today I've talked

about synchrotrons x-rays pigments

Archaeopteryx see Sanctus many different things and hopefully you've been able to

take something away from that today and how we've brought together two worlds of

particle particle accelerators and paleontology to understand more about

ancient life and how we've gone from

looking at the x-rays generated from a particle accelerator to help us identify

the chemistry the elements presence within a fossil and how those elements

might be associated with specific biochemical properties of an animal in

this case pigments now we've done a lot of other research using the signature on

not just looking at colors and we've studied lots of other different types of organs such as plants bones manatees dinosaurs

all sorts of things and we may get around talking about those at the Q&A on the second so please join us then and

thank you very much for that so before we sign off I just want to

acknowledge a few of the few of the people involved in this research so aloes more than what's represented here

but I just wanted to point out that this research and the results that I've

described today are only possible due to the combined efforts and expertise of people from a variety of different

fields because we've talked about particle accelerators x-rays biology biochemistry paleontology and it's only

really with the combination of experts from each of these fields that we are able to come up with the conclusions that we do so just to point out some of

the key people in the research group that's Phil Manning who's the lead paleontologist from the University of

Master in the UK Roy regalia the lead jew chemist and Hoover Bergman the physicist in our group from SLAC

National Accelerator Laboratory

on a personal note I just want to do a big shout out to my mum and dad Malcolm

and Teresa who supported me throughout the years on my desire to become a

paleontologist supported me both emotionally and financially and I wouldn't be where I am today without

their love and support so just to really want to thank them and acknowledge their contribution


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Discovering the Colors of Fossil Creatures

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