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Dinosaur vision reconstructed in a test tube

By Humuhumunukunukuapuaa in Technology
Sat Sep 07, 2002 at 02:19:49 AM EST
Tags: Science (all tags)
Science

Recovering DNA from fossils has turned out to be an extremely difficult task because samples older than a few hundred years old have generally degraded too much to be useful. However researchers in the US have tried an alternative approach - using a maximum likelihood approach to reconstructing a protein from Archosaurs, the ancestors of dinosaurs.


Proteins are built from sequences of amino acids coded by DNA sequences. Over the generations these DNA sequences aren't inherited 100% perfectly but may occasionally mutate. Given the DNA sequences from many different organisms alive today it is then feasible to ask "What is the most likely amino acid sequence that this particular organism might have had given the sequences its currently living descendants and the descendants of its ancestors might have had?"

The researchers chose to work with a form of the protein Rhodopsin. This is the light sensitive pigment protein at work in the rods of the retina and is specialized for high sensitivity in low light level. They took the sequences for 30 organisms alive today (including humans, lampreys, chickens and goldfish) and aligned them using a package called ClustalW. This process is somewhat akin to performing diffs between a set of files (or an agrep between strings). Protein sequences are like software in that there are different portions of the sequence that perform different functions. Alignment attempts to line up each of the different sequences in such a way that the regions that perform a similar function (and so have a similar amino acid sequence) line up together. Alignment algorithms are typically use a dynamic programming approach to find the minimum number of changes (usually weighted in some way) to convert one sequence into another by changing individual amino acids or inserting/deleting subsequences.

Once the sequences were aligned it was then feasible to estimate the sequences that a particular ancestor had. For example if in an alignment we found that the same amino acid always occurred in the same place in every sequence we can be almost certain that it was present in the archosaur sequence. If on the other hand a particular amino acid occurred in many close relatives of the archosaurs but not more distant ones we would be confident, but not certain, that it was the one that appeared in the archosaur. By having a model for the probability of any particular mutation we can determine the sequence with the highest likelihood. This was carried out using a package called PAML.

Once the most likely sequences were determined the protein was synthesized de novo (ie. from scratch). It could then be tested for light sensitivity. Unlike proteins that trigger behaviors like nesting or control development pathways like homeobox genes, rhodopsin can be tested directly in the laboratory for light sensitivity giving an immediate determination of the light sensitivity of archosaur vision. The results of testing indicated that these proteins were similar to modern bovine rhodopsin although their light sensitivity was red-shifted. The precise spectral response suggests that archosaurs had eyes adapted to vision in low light levels and may in fact have been nocturnal.

This experiment has opened up an exciting new way to investigate the physiology and behavior of prehistoric organisms such as dinosaurs. Armed with a computer and a sequence database researchers can now probe our genetic ancestry in a practical way without relying on fossils. And it allows us to determine organism features that couldn't possibly be determined from fossils.

References

[1] BBC Science News (http://news.bbc.co.uk/1/hi/sci/tech/2237114.stm).
[2] Recreating a Functional Ancestral Archosaur Visual Pigment, Chang, Jonsson, Kazmi, Donoghue and Sakhmar, Mol. Biol. Evol. 19(9):1483-1489, 2002

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Related Links
o Archosaurs
o ClustalW
o PAML
o homeobox
o database
o http://new s.bbc.co.uk/1/hi/sci/tech/2237114.stm
o Also by Humuhumunukunukuapuaa


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Dinosaur vision reconstructed in a test tube | 26 comments (20 topical, 6 editorial, 0 hidden)
Any particular reason why (5.00 / 1) (#2)
by Rogerborg on Fri Sep 06, 2002 at 07:05:26 PM EST

We can't just inbreed chickens to throw up regressive genes, and keep selecting the ones that turn out more like raptors?  Chickens are cheap, small, and they breed fast.  Plus they're good eatin'!

Is there a flaw in that basic idea, or is it just that it's too low tech and gradual to attract money?  I recall an old Soviet program that just bred hundreds of foxes until they got one that actually liked people.  The idea of pet foxes never took off, but pet raptors, now that's a banker.

"Exterminate all rational thought." - W.S. Burroughs

Simply take too long. (none / 0) (#6)
by Xeriar on Fri Sep 06, 2002 at 08:25:36 PM EST

It takes around a hundred generations to cause any respectable amount of speciation. To engineer a chicken into a raptor that way would probably take millions of years.

Would be easier just to wait for a computer powerful enough to model the proper genetic sequence for the thing, and make it.

That said, we're already doing this, sort of, in biological warfare and dog breeding. For the love of all that is good and holy, what whacko made poodles? Ugh.

----
When I'm feeling blue, I start breathing again.
[ Parent ]

Got data? (none / 0) (#16)
by Rogerborg on Sun Sep 08, 2002 at 10:57:02 AM EST

    It takes around a hundred generations to cause any respectable amount of speciation.

Depends how you define speciation.  There's a blithe assumption that chihuahuas and great danes are fertile, but who's testing it?  And while dog behaviour appears consistent, remember that dog breeders selectively breed dogs that display the traits they want, and that includes human-friendly pack behaviour.

It's the example of dogs that interests me specifically, because it's done through inbreeding, not through mutations.  Wolves carry the same genes that create a chihuahua, they just don't express them (or the expressives don't survive).


"Exterminate all rational thought." - W.S. Burroughs
[ Parent ]

I saw a documentary once... (none / 0) (#7)
by fluffy grue on Fri Sep 06, 2002 at 09:24:35 PM EST

It may have been the "Dinosaurs" series on PBS a few years ago... basically, there was this one research place where they were using crude genetic engineering techniques to "switch on" dinosaur traits in various birds. Their most "advanced" bird was like a big turkey, only with a raptor's tail and teeth and claws and such.

It was pretty neat, even though it looked really awkward. :)
--
"Is a sentence fragment" is a sentence fragment.
"Is not a quine" is not a quine.

[ Hug Your Trikuare ]
[ Parent ]

I saw a different documentary... (5.00 / 1) (#12)
by Ruidh on Sat Sep 07, 2002 at 12:13:44 PM EST

...where they actually bread dinosaurs from DNA extracted from mosquitos preserved in amber. They gave them a whole island to run around on until their controls broke down and they started eating the staff.
"Laissez-faire is a French term commonly interpreted by Conservatives to mean 'lazy fairy,' which is the belief that if governments are lazy enough, the Good Fairy will come down from heaven and do all their work for them."
[ Parent ]
Wow, cool! (none / 0) (#13)
by fluffy grue on Sat Sep 07, 2002 at 12:43:55 PM EST

Except the documentary I saw wasn't fiction!
--
"Is a sentence fragment" is a sentence fragment.
"Is not a quine" is not a quine.

[ Hug Your Trikuare ]
[ Parent ]

well.. (3.00 / 1) (#9)
by Work on Fri Sep 06, 2002 at 09:48:07 PM EST

by the time that happened, the chickens would probably have developed some survival threatening mutations. It doesnt take too many generations of inbreeding to introduce some really bad problems.

Like the amish for example, 200 years of inbreeding have developed in extremely high levels of mental retardation in newborns, as well as other normally rare genetic diseases.

[ Parent ]

Amish (4.00 / 1) (#11)
by Merk00 on Sat Sep 07, 2002 at 09:29:40 AM EST

I'd really appreciate a citation for your reference to the Amish inbreeding causing high levels of mental retardation or other rare genetic disorders. The "inbreeding" among the Amish isn't really all that great. Usually, marriage, when it takes place between relatives, takes place between rather distant relatives (something like 6th cousins). This really is no different from a lot of what happens in small towns normally. From the Amish I do know about, I've never heard of birth defect problems because of inbreeding.

------
"At FIRST we see a world where science and technology are celebrated, where kids think science is cool and dream of becoming science and technology heroes."
- FIRST Mission
[ Parent ]

from memory... (none / 0) (#14)
by Work on Sat Sep 07, 2002 at 02:38:54 PM EST

a few weeks ago i was reading a story about the high levels of autism that pervade amish children, one particular family has had 4 children, all severely retarded. The genetic issue with the amish is well documented...a google search will turn up hundreds of sources.

[ Parent ]
Polydactyly (none / 0) (#26)
by toganet on Thu Oct 17, 2002 at 05:46:55 PM EST

The only genetic trait I've seen tied to Amish communities is polydactyly (extra fingers/toes).

This is due more to the fact that the original Amish population was made up of a larger-than-normal number of polydactyls than the general population.  The usual rate is about 2 per 1000 live births, and is commonly "corrected" within 1 year of birth, depending on severity.

Johnson's law: Systems resemble the organizations that create them.


[ Parent ]
Chickens != people (none / 0) (#15)
by Rogerborg on Sun Sep 08, 2002 at 10:49:38 AM EST

    by the time that happened, the chickens would probably have developed some survival threatening mutations. It doesnt take too many generations of inbreeding to introduce some really bad problems.

Why would you let the failures breed?  You just eat the ones you don't like and only breed the good ones.  If that sounds harsh, do some reading on how "new" dog breeds are created.


"Exterminate all rational thought." - W.S. Burroughs
[ Parent ]

The Amish (5.00 / 1) (#20)
by Khedak on Fri Sep 13, 2002 at 02:08:19 PM EST

I think it'd be a little more fair for you to distinguish between certain Amish communities and "the Amish" as a collective whole. The connotation of your blanket generalization is insulting to those of us who never wear buttons but have got a cool hat.

[ Parent ]
No buttons (none / 0) (#25)
by Cwis on Fri Sep 20, 2002 at 06:09:26 AM EST

But they get to party like it's 1699.

[ Parent ]
Friendly Foxes (none / 0) (#24)
by MyrddinE on Tue Sep 17, 2002 at 08:19:18 PM EST

Amiable and tamable canines tend to have floppy ears and less defined mothering instincts.

Scientists believe that this is because that breeding for doglike characteristics actually is breeding for immaturity in the animals. We are breeding for a subspecies of canine that does not fully mature. Hence, the floppy ears (characteristic of fox young, aka kits) and the underdeveloped breeding instincts.

The same characteristics occur when you breed for tame wolves... you get dogs. I do not know if research has been done to see if this same taming=immaturity rule applies to families other than doglike ones.

[ Parent ]

Great! But... (none / 0) (#3)
by notcarlos on Fri Sep 06, 2002 at 07:18:59 PM EST

What use is this? So we have the 'most likely' vision sequence for an archosaur. It doesn't mean that we've got the actual vision proteins for anything -- it's just something built in the lab based on statisitics and probability, two tenuous and highly constructed fictions at best. The only way you will know if it worked is if you find one, either Dioxyribonucleically or in some prehistoric valley.

He will destroy you like an academic ninja.
-- Rating on Rate My Professors.com
Good question (none / 0) (#18)
by darkskyes on Wed Sep 11, 2002 at 02:48:55 PM EST

and something that would've been nice to see in the article. This technique may be more accurate(resulting from previous tests) than just educated guessing. I'm not claiming that as fact, I'm saying it would be a good thing to check on.

I'll try to do so, but I am suffering from a crashed RAID array headache compounded by a broken backup tape infection. So it may be awhile before I have that much free time...

-"Your disadvantage is that you will always, always be outnumbered, and ...your enemy will learn more about you, how to fight you, and those changes will be put into effect instantly." -Mazer Rackham
[ Parent ]

"Knowledge is Good" (none / 0) (#21)
by inadeepsleep on Sat Sep 14, 2002 at 08:20:34 PM EST

Everyone isn't as concerned with immediate applicability as you seem to be.  And I'm glad about that, otherwise scientific progress would slow to a crawl.


[ Parent ]
Well, now (5.00 / 1) (#22)
by notcarlos on Sun Sep 15, 2002 at 04:03:32 PM EST

I'm not saying I'm against unapplicable knowledge, it's just that, well, this wasn't exactly a question that was a big issue for me. Must you be so universal? Geez.

He will destroy you like an academic ninja.
-- Rating on Rate My Professors.com
[ Parent ]
sorry n/t (none / 0) (#23)
by inadeepsleep on Sun Sep 15, 2002 at 09:44:49 PM EST




[ Parent ]
Redshift ? (1.00 / 1) (#19)
by alternatist on Fri Sep 13, 2002 at 04:10:23 AM EST

The results of testing indicated that these proteins were similar to modern bovine rhodopsin although > their light sensitivity was red-shifted.

... the same amount as light from stars 250 million lightyears away ? just a crazy idea ...

Dinosaur vision reconstructed in a test tube | 26 comments (20 topical, 6 editorial, 0 hidden)
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