Reconstruction of Ancestral Proteins

Michael Behe would say that this is an uninteresting result. Completely trivial. Not surprising--no, not at all. In fact it's downright boring. Getting sleepy now, ... zzzzz.

There are older references as well concerning ancestral reconstruction. All of them are exciting to me. It's like the ultimate form of paleontology and you don't have to get sunburned doing it!

jeh: Michael Behe would say that this is an uninteresting result. Completely trivial. Not surprising--no, not at all. In fact it's downright boring. Getting sleepy now, ... zzzzz.

Contrast this with Intelligent Design, which has yet to make a useful prediction of any kind.

— Ian Musgrave

But it's still a protein! (Well, someone had to say it).

Seriously, the ID crowd will probably just say that you can never be sure if you are right or not unless you find the "missing links". Of course, some will eventually be found and sequenced, so then they will have to retract their statements and admit that science was right and that they were wrong all along. What? Oh yea, I forgot, they'll never read the papers. Never mind.

David Stanton: But it's still a protein! (Well, someone had to say it). Seriously, the ID crowd will probably just say that you can never be sure if you are right or not unless you find the "missing links". Of course, some will eventually be found and sequenced, so then they will have to retract their statements and admit that science was right and that they were wrong all along. What? Oh yea, I forgot, they'll never read the papers. Never mind.

That sounds like they're working a jigsaw puzzle that has lots and lots of pieces, and no picture on the box to show what it's gonna look like when done.

Henry

I proposed doing the same thing decades ago. Not with bacteria. With dinosaurs. In theory with enough phylogenetic sequence information we should be able to reconstruct the genome of...dinosaurs.

From there it is a simple genetic engineering problem to recreate large extinct reptiles.

I'm tempted to say that Spielberg and Crichton stole my idea for Jurassic Park, but they came up with it independently and much later.

In practice one doesn't need the whole genome, just the controlling morphogenetic/developmental biology loci. It will most likely be harder than it sounds at first glance but Jurassic Park is coming within the grasp of modern science.

That's a seriously hot ocean! Thanks for the informative post.

But you have to already have faith in evolution and naturalism to get such a result. You know, sort of like having to have faith in the second law of motion before you can calculate the thrust of a rocket.... Oh, uh, never mind that.

The most important thing is that you can't ever show that a designer didn't have something to do with the course of the changing proteins, so ID will always be science. I'm ready for my awards for pointing this out, and the textbook orders for my book. They'll save money, too, since it only takes a couple of pages to point out that a designer could have done things without being detectable, and to figure out that God did it from that.

And you guys thought science was hard, and a lot of work. All of that useless sequencing and hypothesizing, and it's still altogether too plain that you can't rule out a designer. Don't you feel foolish now!

Glen D

http://tinyurl.com/3yyvfg

Technically with sequence data it is quantitized so it is possible to get around the multiplying gaps sophistry.

They have a trivial tactic for dealing with no-longer-missing links, because the more links you have, the more “gaps” there are between them.

— Nigel D

JGB: There are older references as well concerning ancestral reconstruction. All of them are exciting to me. It's like the ultimate form of paleontology and you don't have to get sunburned doing it!

But, where are the Neutral Gaps ?

I think that the study may be being misinterpreted. Really what is being argued is that the earliest-diverging lineages of *extant* life lived in hot environments. Taking a step from there to saying that the oceans were hot is another step. One might argue an alternative view, e.g. that what this study shows is that the ancestors of modern life developed some key features while living in high-temperature environments, and subsequently spread out and beat out all of the other microbial life forms then existing.

(I have also seen it argued that the basal-thermophile observation is an artefact due to DNA & amino acid sequences changing more rapidly due to e.g. adaptation from moderate to extreme environments. I assume the authors thought about that & dismissed it for reasonable reasons but I haven't looked into it.)

Also -- I have seen claims that global glaciation events are known in the precambrian geological record, how does that match up with the geological evidence for higher temperatures?

The Hadean eon lasted until 3.8 billion years ago:

http://en.wikipedia.org/wiki/Hadean

and is currently thought to be life-free. The Paleoarchean era is currently thought to contain the earliest fossils but there is no evidence of glacial activity:

http://en.wikipedia.org/wiki/Paleoarchean

The earliest definite evidence for massive glaciation (of which I am aware) is much later, during the Neoprotozoic era:

http://en.wikipedia.org/wiki/Neoproterozoic

by which time life forms had been evolving for about 3 billion years.

Oh, oh!

Don't you get to use the "blogging reviewed literature" thingy? I think you should, if only to piss-off Casey Luskin. Piss-on, piss-off, kind of like the Disko Kid.

Ian Musgrave wroteHow can you reconstruct the protein sequence of organisms long gone? Using evolutionary theory, you can take the genomes of existing related organisms, and work backwards to the sequence of their common ancestor.

The simplest way to do the reconstruction William is using an established phylogeny and then using a parsimony analysis. The more sophisticated approach would involve Maximum likelihood methods. Either approach faces substantial uncertainty at poorly conserved residues, but these days it is feasible to analyze a number of these mutations to check for what presumably in most cases (though not all because of the potential for epistasis) are neutral or near neutral variants. The statistical methods and molecular techniques have improved but the idea is atleast as old as an Emile Zuckerkandl and Linus Pauling paper on hemoglobin from the 60's

"More specifically, how can you know that you’ve reconstructed the protein sequence?"

We can never "know", we can only make reasonable inferences based on current data.

"If I simply assert that super studly researchers at the von Trap institute for linguistics have reconstructed the pre-historic word for dwelling by using linguistic theory, and extrapolating backward in time words for dwelling including: woning, σπίτι, Wohnung, домашн, domestico, moradia, κατοικία, and жилище, and came up with wπмmestοιщеung, many would consider this little more than pseudo-scientific technobabble."

Imagine that you have a robust linguistic theory of which letters tend to change into other letters and at what likelihood. At every stage of the reconstruction, imagine that you have ways to check if the reconstructed word would have been likely to be a real, usable word in a real language, or a non-viable chimera (as your ancestral word seems to be).

Nick (Matzke): I think that the study may be being misinterpreted. Really what is being argued is that the earliest-diverging lineages of *extant* life lived in hot environments. Taking a step from there to saying that the oceans were hot is another step.

This analysis can’t determine whether the organisms were living in hot springs, or if the entire oceans were hot, but the thermostability of the proteins correlate strikingly with oceanic temperatures inferred from oxygen and silicon isotope ratios.

William,

In fact linguists have done precisely that, just google proto-indo-european language. By gathering all languages of the indo european language tree, and also written records of extinct indo-european languages, focusing on words that would exist since the start, such as 'mother', 'father', 'goat', 'dwelling', etc. Linguists has reconstructed the best approximation of the progenator of indo-european languages. Along the way the most probable phylogeny is also reconstructed. Since writting came after PIE (proto-indo-european language) any written version of PIE is merely a transliteration.

William Wallace: I am still waiting for an answer. How can you reconstruct the protein sequence? This is a legitimate question. More specifically, how can you know that you've reconstructed the protein sequence?

More specifically, how can you know that you’ve reconstructed the protein sequence?

You got to love science, who takes its results through as many tests as it can come up with. As opposed to, say, creationism btw.

— Torbjörn Larsson

Nick (Matzke) said:
"Also – I have seen claims that global glaciation events are known in the precambrian geological record, how does that match up with the geological evidence for higher temperatures?"

Global mean temperatures are may not be very relevant. Shortly after an initial crust solidified, there were almost certainly places that were very hot for a very long time. The mid-atlantic ridge is one such contemporary example.

the human pseudogene for chlorophyll.

windy wrote: We can never “know”, we can only make reasonable inferences based on current data.

William Wallace:

windy wrote: We can never “know”, we can only make reasonable inferences based on current data.

Thanks to you and others. Sounds like an interesting parlor trick all and all, but short of a time machine, it doesn't sound exactly falsifiable. William Wallace

Thanks to you and others. Sounds like an interesting parlor trick all and all, but short of a time machine, it doesn’t sound exactly falsifiable.

They "recreated".....?!?

I don't think you should use the word "creation."

It should have said they "randomly facilitated a random repeat of something that happened..."

Of course we all know it could have never randomly happened. There has to be some creation... just like everything else.

They “recreated”…..?!? I don’t think you should use the word “creation.”

William Wallace,

Skimming your new blog I can see a little better why the DI is giving up the pretense that their ideas are motivated by anything but a religious right ideology. Nevertheless I respect your religion and political POVs; I probably agree with you more than not on the latter, and I also am a theist if not a member of any organized religion.

My questions for you, however, have nothing to do with any of that, or any of the ID sound bites that you like, or any problems with "Darwinism" you may have. Rather I'm only interested in whether you agree with Michael Behe that:

1. Life on Earth has a 3-4 billion year history.

2. Modern humans are related to other animals, plants, etc.

Note that neither answer requires that you accept a Darwinian mechanism. And even if you are genuinely unsure, you seem confident enough in your other ideas that you could easily offer a "best guess." If you have answered those questions elsewhere, a link will suffice.

Thanks in advance.

I THINK ITS REALLY VERY EXCITING & INTERESTING, ITS REALLY NEW, SO FAR I HAVENT CAME ACROSS ANY SUCH ARTICLE ELUCIDATING & RECONSTRUCTING A BACTERIAL GENOME, BUT ONE THING I WANT TO KNOW IS WHICH GENOME U HAVE RECONSTRUCTED (which bacteria)& CAN I GET SOME MORE DETAILS ABT THE SEQUENCING PROCEDURE & METHODS ... KINDLY REPLY ON dimri_amita@rediffmail.com

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I understand the logic behind inferring a higher likelihood for warmer oceans at an earlier time vs colder. I don't understand the logic Ian is using to attack ID by saying the proteins fold. Wouldn't you expect the product of something as similar as prokaryote elongation factors are to eachother to fold? It's like saying we took the parts from 25 different Ford Mustangs, and we were able to make a car that looks very much like a Ford Mustang - in fact it even runs!

I mean, are you really expecting to disrupt even a secondary structure when you already know those domain sequences already come from functional proteins that are nearly identical?

Isn't stasis the opposite of evolution?

I guess a better way to understand my question is, if it took 3 billion years for an elongation factor to evolve into an elongation factor, then how long did it take for elongation factors to evolve in the first place? I could see trumpeting these results if modern EF-Tu's varied widely, and after a regression was done, a protein with a similar function but a distinct shape was produced. Isn't this is what evolution would predict if these proteins aren't "islands of function"? It seems a little counter intuitive that these things worked so well at the beginning, that the only changes that were tolerated in billions of years were substitutions that cause it to become less stable. Doesn't it seem weird to anyone that this protein is evolving to be less stable when the extra metabolic cost of needing to create more replacements for something as critical as EF-Tu (the most common protein in bacteria) should select for versions that produce a more stable fold? How can this be discounted if we want to say that evolution went so far as to refine EF-T to remove the spent GDP from EF-Tu? If natural selection is powerful enough to do that, certainly it could choose from between more robust or less robust forms OF THE SAME PROTEIN - forms we have now demonstrated can exist!

brain... hurts...

too... much... gibberish.

dude, take your anti-adhd drugs or something, eh?

you make no sense, at all.

I tried running your post through the gibberish translator:

http://mybigmonkey.com/gibberish/

but you must be using a peculiar dialect of gibberish.

John said: Isn't stasis the opposite of evolution?

So if a cat gave birth to a dog, evolutionists would give up in defeat? Or would the hopeful monster no longer be hopeful? I think we all know the answer.

Evolution = change over time, and evolution = no change over time. Behold the testable predictions of evolution. Now I see why "everything in biology makes sense in the light of evolution".

Geology: erosion and other forces may transform the landscape over a short period of time (see "Dry Falls, Washington"). Or some landscape features may last a very long time.

"Geology = rapid change over time, geology = slow change over time. Behold the testable predictions of geology."

Evolution is "descent with modification," not "change over time."

What I'm trying to say is that the same forces that can encourage rapid modifications can, just as easily, discourage rapid modifications.

Furthermore, not all evolutionary modifications or changes are readily apparent. For example, fossils of okapis suggest that, back in the Miocene, they looked pretty much identical to modern okapis, except that back in the Miocene, okapis lived in tropical woodlands and grasslands, rather than dense rainforests, and that they probably organized themselves into herds.

Or, better yet, John, please explain why you would you consider a species to have "not evolved" when it has forces constantly selecting against any deviation from the ancestral form? Even if these same forces might cause another species to deviate radically from the ancestral form?