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Creating Artificial Proteins
Spy der Mann writes "By examining how proteins have evolved, UT Southwestern Medical Center researchers have been able to design genes to create artificial proteins.
The researchers have discovered a set of simple "rules" that nature appears to use to design proteins. By feeding these rules into a computer program, they were able to obtain a sequence of artificial genes. These genes were then inserted into laboratory bacteria, producing the artificial proteins as expected."
I've been creating proteins by hand since I was 12!
Norman Cook's Ode to Sl
Hopefully we'll figure out what not to say while learning the grammar, style, and syntax of this new language. It's a bit worrying -- but this really has a lot of potential, I think!
Paleotechnologist and connoisseur of pretty shiny things.
This seems like a very, very simple way of tagging people. I.E., if you can make a protein that can't occur in the body naturally, inject it into someone when you do something to them. Kind of like having the P on the wrists of pirates, except it avoids all those "social stigmatization" arguments... but allows foreign governments (or whoever) to see that they've been marked. Interesting....
Isn't one of the reasons that creationist use when they attack evolution (actually abiogenesis) is that it would take such a long time to generate functioning proteins through random chance that it would be statistically impossible? If there are simple "rules" to create proteins, maybe that's how nature was able to come up with life so quickly.
Real_men_don't_need_spacebars.
Does anyone know what Roland Piquepaille thinks about this?
More importantly, does anyone care what Roland Piquepaille thinks about this? About anything?
The higher the technology, the sharper that two-edged sword.
amino acids
"Hel-l-l-p me-e-e-e-e..."
Seeing bad movies only encourages them. Watch responsibly
Well, we know we've been able to modify DNA to produce insulin from bacteria.
We've got bacteria that crap out metal wires (Can't remember if we discovered them or made them)
Now where's the bacteria that will make substances like xanax or other drugs, so it can make the entire market cheaper and more affordable to those who need it but don't have insurance, and "naturally" at that? (Naturally as in not needing a buttload of power from a processing plant for the drug and wasting energy uselessly)
Still waiting on Serviscope_minor to wake up to fucking reality and realize that Jessica Price isn't going to fuck him.
I think you might be using backwards logic here. TFA states that by examinig 100 proteins they were able to notice some standard common things about the proteins they were looking at. When they made rules around those common things they could make new proteins.
It's like having 100 pieces of example code to look at before trying to create your own, not generating the code from nothing.
s
And the answer to this could be that a lot of rules have been randomly tried out. It turns out that the rule(s) we are seeing/discovering are the ones that lasted - and if they are simple they are probably efficient in some way.
The creationist/ID policy is to avoid facing unknowns by passing the buck onto a designer. In the current example, just because something appears elegant and simple to some person, it does'nt mean that it could not have naturally occured.
Our jobs, as scientists, or in the more general case, as people with a scientific temperement, is to uncover how or why this simple and elegant thing is the way it is - not to say, 'It's too tough, lets pass the buck onto the designer'!
The researchers believe they may have found a set of statistical rules for determining the tertiary ('overall') structure of proteins from the sequence.
(Although the summary reads otherwise, creating a 'new' protein with an arbitrary amino acid sequence isn't new at all though. )
If this pans out, it is of course significant towards the goal of engineering 'new' proteins one day. But there is still a lot to be covered. Even if the relationship between sequence and structure were simple and known (and it isn't, yet), you still have the issue of relating structure to function.
Which isn't known. And of course, even knowing the structure and function of a single protein doesn't mean you know what it's going to do in a complicated environment such as a cell, where there are thousands of things to interact with.
It's a step forward, nonetheless. But if someone thinks this means we're going to be tricking-out living organisms with new custom-engineered proteins anytime soon, you'll be disappointed.
Only the cash-strapped slashdot editors
Their "rules" were derived from observing nature, not computed or by any ab-initio means.
The original summary of the article is quite off base, as many of these biochemistry-related revelations are.
I would better summarize the Nature paper as saying that the researchers have found a somewhat reliable method of duplicating a three-dimensional structure by using existing sequences as a simple template. The concept of truly "designing" a protein from scratch remains the Grail of this field.
her hairy back?
Artificial proteins! YES! One step closer to Artificial steak!
...On a hardwood floor? Oh, it's you Zonk...
"Who are in control, they are not in control of anything - they don't even control themselves!" - Glen Beck
For once, this is not the place. The rules are not as they seem: too much is still unknown.
Can this be used for information compression in any way? After all, it was discovered about 20 years ago that simple fractal equations gave shapes very much like ferns. This could give you a shorthand way of compressing the genome of an organism, then making comparisons.
It would also, of course, be interesting if you could use this to work backwards through the genome to a set point, and (hypothetically) bring back the Auroch.
Personally, I want to see how this deals with metal incorporation at the active site, and whether their selection rules work for that as well.
the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
The project headquarters in Raccoon City reported spectacular progress in the manufacture of artificial virii that may have substantial medical and humaniatarian uses, as well as minor military applications.
I believe that this is just the start of engineering a new race of superhumans (saiyans). Hopefully I'll be one of the ones they test on, I have always wanted to throw a spirit bomb at my biology teacher! I'm not quite sure if this is me talking or just the marijuana and gin-- I mean cold medicine marijuana use and under age drinking are illegal.
How long before gcc supports this new instruciton set? :p
What it is more likely to imply is that many (maybe all?) proteins seem to share the same basic "rules" in their construction, therefore nature only had to come up with a few workable combinations, and everything else was developed from that.
:)
Note that these "rules" are defined by the scientists based on observation and not necessarily actual, natural restrictions. A lot of creationists seem to fall into that trap when defining species - the concept of "species" is a completely man-made concept and actually rather arbitrary. Nature does not make any such distinction. So just be careful... they say there are "rules" but don't go thinking nature is somehow obliged to play be them
=Smidge=
Full text of article, institutional/personal subscription required.
Abstract: Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. Here, we attempt to define the sequence rules for specifying a protein fold by computationally creating artificial protein sequences using only statistical information encoded in a multiple sequence alignment and no tertiary structure information. Experimental testing of libraries of artificial WW domain sequences shows that a simple statistical energy function capturing coevolution between amino acid residues is necessary and sufficient to specify sequences that fold into native structures. The artificial proteins show thermodynamic stabilities similar to natural WW domains, and structure determination of one artificial protein shows excellent agreement with the WW fold at atomic resolution. The relative simplicity of the information used for creating sequences suggests a marked reduction to the potential complexity of the protein-folding problem.
From this page : a WW domain is the smallest, monomeric, triple-stranded, anti-parallel beta-sheet protein domain that is stable in the absence of disulfide bonds, cofactors or ligands.
I would definately eat artifical steak. I'd also like to try a wide range of other engineered vegetables.
Yes, I also ate paste in kindergarten, but also so did YOU.
Zhrodague.net - I do projects and stuff too.
Why can't these articles include any meaningful information? They refuse to tell you what they're about.
Earlier research has shown that for a given group of related proteins, or protein family, all family members share common structures and functions.
What would be an example of a "protein family" in this context? Filamentous? Membrane associated? Globins? Antibodies? No idea. "Common structures and functions" could mean several different things.
By examining more than 100 members of one protein family, the UT Southwestern group found that the proteins share a specific pattern of amino acid selection rules that are unique to that family.
This tells us nothing that isn't already known. Of COURSE proteins with related functions share specific patterns of amino acid selection rules or they wouldn't work. WHAT sort of selection rule did this group actually find?
"What we have found is the body of information that is fundamentally ancient within each protein family, and that information is enough to specify the structure of modern-day proteins," Dr. Ranganathan said.
He sounds like he's talking to a little kid.
He and his team tested their newly discovered "rules" gleaned from the evolutionary record by feeding them into a computer program they developed. The program generated sequences of amino acids,
and how did it do this?
which the researchers then "back-translated" to create artificial genes.
i.e. they did a trivial replacement of single amino acid letters with three letter codons in silico, then generated the corresponding DNA sequence.
Once inserted into laboratory bacteria, the genes produced artificial proteins as predicted. "We found that when isolated, our artificial proteins exhibit the same range of structure and function that is exhibited by the starting set of natural proteins," Dr. Ranganathan said. "The real test will be to put them back into a living organism such as yeast or fruit flies and see how they compete with natural proteins in an evolutionary sense."
Translation from stupid-articlese: in vitro the translation products of the artificial DNA folded into shapes similar to wild type proteins. I think.
One can only assume that these guys chose proteins that don't undergo post-translational modification.
Hey, I guess Intelligent Design was just ahead of its time.
Retired from software... maybe. Sort of.
maybe now all us anime/manga fans can rejoice and change the hair color of our kids to sky blue, sea green, or bubblegum pink, or some other outlandish color like purple
Viable Slashdot alternatives: https://pipedot.org/ and http://soylentnews.org/
If that was all they'd done I find it difficult to see how this differs from doing a multiple sequence alignment for a family of proteins, then making a gene for the consensus sequence.
Checking the paper (and related News and Views article) in Nature itself (http://www.nature.com/nature/journal/v437/n7058/i ndex.html ) (subscription required) indicates they've done more than that. By including the effects of coevolution - where one position in the protein mutates in concert with another to maintain optimal contacts - they generate a substantially better algorithm for manufacturing particular folds. (ie: 25% success in achieving folding versus 0% for conservation alone. 60% presence of wild-type function in the 'designed' proteins.)
Interesting, but I'm suprised it made it into Nature. (OK then, jealous...)If you want to see what three lines of code plus a few random numbers can create, search for a Java applet that implements the "Hopalong" algorithm.
Mankind created happy little protein-building bacteria. And it was good.
I am scientifically inaccurate.
"If there are simple "rules" to create proteins, maybe that's how nature was able to come up with life so quickly."
OK...but who/what is nature to develop/come up with these rules? The argument your trying to debunk is that they couldn't be created by chance....there is nothing chance about having "rules" to create proteins...and for that matter...order.
Every time someone uses experiments like this to "disprove creationism" (as if this is something that can be proven or disproven in the first place), they ignore the common feature to all of these tests:
The scientist.
All this "proves" is that it is possible for an intelligent being to combine elements to create something more complicated.
You're saying this experiment shows all of this around us "proves" it could all happen on its own?
Artificial protein has been around for ages and never gets old. Amazing!
The rules for how DNA encodes protiens have been known since before I was born. The evolutionary mapping of how the genes coding different protiens duplicated and evolved into new structures is fairly easy to map out (give or take a brute force algorithm that runs in double-factorial-time to search through all evolutionary trees looking for the one that minimizes the number of mutations required along the way).
So this group has calculated the most likely common ancestor of the gene that now codes for a whole family of protiens, encoded the solution in real DNA, stuck it into bacteria and shown that it actually does produce a protien that they have been able to isolate the actual protien so that they can explore what it does/did.
(the term "articial protien" seems very odd to read - before I think it through, it sounds as though its hinting there is something mystical to "natural" protiens untouched by humans)
While I realize this news seems fascinating to some individuals, it is not something so entirely new that people in Computational Biology would consider it groundbreaking. Using the computer algorithms to generate new gene sequences is actually just a matter of running the gene finding algorithms you used to find these genes backwards (in fact, many people have been testing their gene finding algorithms by using their old algorithms to generate pseudo test sets). The only thing new about this paper is that people actually went forward and experimentally validated their results. An interesting find, however, the end result does not provide a huge leap to science.
Now, if people are really interesting in some neat ways of reengineering genes back onto themselves, then they should take a look at some of the work being done with synthetic circuits. The beauty of synthetic circuits is that since you already know how the genes will function, it's just a matter of setting the circuit up in the fashion that you want so that it produces the end result that you want. There really is no limit to what you can do with synthetic circuits (of course, researchers have a long way to go before they master and understand all the regulatory mechanisms). For example (and these are all very theoretical examples): building a cell circuit to release a drug into a body in a very time released fashion (and perhaps autonomously renewing, for example, building a circuit to release insulin into the body given the sugar level of the individual), designing a circuit to recognize and destroy tumors (or perhaps an even simpler form of designing a circuit to recognize and fluorescently label tumor cells in the body helping in removal/early detection). Of course, one could also build quite malicious synthetic circuits as well. For example, a circuit that would aggregate to the wall of the heart and, after a certain number of other cells accumulate, triggering a signal to all the malicious cells and destroy the heart in unison.
The other nice advantage of synthetic circuits is that the more we learn out regulatory mechanisms in species, the more we can use them for synthetic circuits. The more we use them for synthetic circuits, the more we understand about how exactly the underlying mechanism works (what causes them to break, how do they deal with differing toxic environments, etc). It creates a nice feedback loop with the progression of science.
There will come a day where it will be useful to generate new DNA/Proteins in combination with synthetic circuits, but, as noted in a previous post, we don't understand the relationship between protein sequence and structure/function enough for it to be a viable option (and this is just with how the protein folds, we haven't even gotten in to the problem of gene regulatory structures-- multiple gene splicing, chromosome structure elements, binding motifs, translational regulation, etc). In fact, this area is something we probably want to venture into as it provides us with an even finer control over the rate constants for synthetic circuits. But for now, the generation of randomly generated genes based on prior genes will go overlooked for quite some time.
i have no comment other than 'word', very well put.
Its life Jim but not as we know it....
OH MAN I CANT WAIT FOR THE FUTURE! seriously, cyborg fish people with tentacles and hard drive implants, think about it.
I do not pretend to be an expert, or actually know anything about the subject and to promote Slashdot standards on information digesting, didn't actually read the article. But if one creates proteins that are exactly as nature would manufacture the real thing, why are they called artificial? They are the real thing!
In a nutshell Prof. Keasling and these guys are getting E. coli. to make terpenoids cheaply and in large quantites. The first commercial application that amyris is developing is a process for artemisinin, a fantastic anti-malarial drug. Currently, the drug can only be extracted from some plant in small amounts. This bio-synthetic process will (hopefully) lower the cost per dose from ~$USD 2.40 to ~$USD 0.25 (iirc).
Somewhat off topic, but probably still interesting to the slashdot croud is that the commercialization of artemisinin is being paid for by the Gates Foundation.
I believe the term you were looking for was "Crab People".
PDFs of our papers, and Java code implementing 4 different correlated mutation algorithms including SCA, are at my web site:
http://www.afodor.net
The references are:
Anthony A. Fodor, Richard W. Aldrich. On Evolutionary Conservation of Thermodynamic Coupling in Proteins. JBC 279(18):19046-19050, 2004
John P. Dekker, Anthony Fodor, Richard Aldrich and Gary Yellen. A pertubation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics 20:1565-1572, 2004
Anthony A. Fodor and Richard W. Aldrich. Influence of Conservation on Calculations of Amino Acid Covariance in Multiple Sequence Alignments. Proteins 56(2): 211-221, 2004
The last paper contains a comparison between SCA and three other correlated mutation algorithms.
As I said, I haven't had a chance to look carefully or critically at the new papers. (It takes me a LONG time to read a paper critically :-> This Slashdot thread will be likely long archived before I finish thinking about these papers!). But this particular algorithm aside, people who are interested in bioinformatics and contact prediction may find the math behind the correlated mutation algorithms interesting.
Anthony
Email: anthony.fodor(remove this and put in an at symbol)gmail.com
http://www.afodor.net/
no, we already have them-- they're walking all over the strip here in vegas. oh wait, i think you meant more genuinly a crab instead of crabby ;]
Any creation of proteins by scientists does nothing but bolster the arguments of intelligent design theorists everywhere. I don't know why people don't see this immediately, but since you don't I'll spell it out for you. If anyone with an intelligence (such as scientists are wont to have) creates proteins, THAT IS EVIDENCE THAT IT TAKES INTELLIGENCE TO CREATE PROTEINS. The only way that protein creation could bolster the arguments of evolutionists is if proteins were observed spontaneously generating, proven to be without the interference of any intelligent agent. This means that its basically impossible to create any experiement to support biochemical evolutionary theory, since everyone who cares about such things is also an intelligence. The only person who might get some evidence in the milieu that is needed would be an explorer into the unknown with a very powerful microscope.
Before there is a large debate in the ethics community, they (you) ought to get the facts straight.
E. coli is not a virus. Depending on the strain, the genome size is anywhere from 4.6 to 5.2 millions of base pairs. Putting one of your very own E. coli genomes together would be difficult and expensive. Better yet, why not just grow some? They'll spit up their genome after a few biochemical steps at the lab bench. If you were talking about a phage, their genomes are variable, averaging 35-50 kbp, or thousands of base pairs. That's still difficult and expensive. Even when you got your phage genome put together, now what? You need infectous phage particles to go about the infection/replication cycle. Phage particles aren't infectous to mammalian cells, so that's not what the terrorists are after.
Working with and engineering virus particles isn't reliant upon ordering oligos and assembling the entire genome. The hallmark of being a genejockey is allowing the DNA-containing object to do the replication work for you. You let the bacterial culture divide. You let the mammalian cells divide. You let the phages infect the bacteria and replicate. You let the viruses infect the mammalian cells and replicate. You then harvest the DNA from the millions of [whatever], make some CTL+C and CTL+V with some enzymes, and package the DNA back up in the infectous particles. It's a non-trivial process, and the ability to order oligos on the web doesn't magically give someone the ability to hack out a super virus.
It makes... doilies!
"Is life so dear, or peace so sweet, as to be purchased at the price of chains and slavery?" - Patrick Henry
No, they forget that there is no way to disprove creationism because it postulates that the outcome we see would be identical for both evolution and creationism. Creationism is just a fancy explaination for the same observation except it cannot be used to predict anything. You could say that gravity is just the effect of the Flying Spaghetti Monster pushing things downwards and the only difference between your theory and Newton's would be that your's is worthless for telling what an object might do if it's in the air.
Justice is the sheep getting arrested while an impartial judge declares the vote void.
a whole new host of PRIONS for us to endure.
Actually it doesn't prove that intelligence is required, either. All it proves is that intelligence CAN create proteins.
Justice is the sheep getting arrested while an impartial judge declares the vote void.
The creationist/ID policy is to avoid facing unknowns by passing the buck onto a designer. In the current example, just because something appears elegant and simple to some person, it does'nt mean that it could not have naturally occured.
I don't think that's quite correct. My understanding is that ID examines a result using statistical or logical tools to see if it could have occurred by chance. It's not a subjective test. A statistical abberration indicates some outside influence. A collection of pre-existing conditions that all must be met at once (and not a step at a time) indicates some outside influence.
Glib oversimplified statements about ID will only come back to haunt you someday when we realize those ID guys were onto something - even if they don't quite have it all figured out yet.
IF survival of the fittest was true (evolution) then why is there such a biodiversity? Why are there symbioses between stronger creatures and smaller while the stronger do not necessarily need the other creature and can better eat it?
Custom electronics and digital signage for your business: www.evcircuits.com
Hmm. Some time ago, I seem to recall, there was some talk of whether or not the chimpanzee should be considered to belong to the genus homo.
You've just suggested an experiment that would prove once and for all, one way or the other; but somehow, I can't see any chance of it receiving official approval.
Je fume. Tu fumes. Nous fûmes!
Why are there symbiant relationships? It allows for division of labor, essentially. The genetic load of one organism after symbiosis does not have to take care of these certain task that the other is taking care of. Most of the cells contained in your body are not actually yours. The majority of cells in the body are bacteria living in your intestine which each produce proteins which help with digestion. If our DNA had to encode for every one of those digestive and metabolic proteins that are actually used in digestion, we would be selected against compared to an organism that could make more efficient use of its DNA.
Diversity also leads to a sort of long term stability. If there are different ways to obtain resources, the ecosystem as a whole can adapt to environmental changes far more gracefully.
I'll never make that mistake again, reading the experts' opinions. - Feynman
Maybe there is an alternative universe with different {but mutually consistent} rules; where light does not travel in straight lines, the pressure in a fluid acts unevenly and ferric bicarbonate exists in abundance. But we would never know about it, because it would not obey the right set of laws of physics to be observed by us.
Je fume. Tu fumes. Nous fûmes!
Because you dont need to be perfect, just survive :)
The system had the verbosity of HTML combined with all the readability of compiled assembly viewed as bitmap images
Yeah, exactly. Natural selection is pass/fail, there are no As, Bs, etc. :-)
Furry cows moo and decompress.
So...
There are a few basic shapes which perform useful functions.
There are a few "rules" - actually generalities in the mechanisms which have evolved so far - that govern the manner in which more complex shapes and functions emerge. (They're not rules as in "do this, don't do that.)
After 2 billion years, complexity emerges, but still governed as above.
Sorry to break this to you, boys, but Darwen and Wallace got there quite a bit sooner, and this is not a surprise to anyone excepting possibly President Bush and the Wilberforce household.
Be interesting to know what the LUCA proteins were / are though...
"... and more and more now there are all kinds of electronic goodies available" -- Pink Floyd 1972
Except that on rare occasions, Mules are fertile. Now what?
Also, although I am not aware of any attempts (much less successful ones) at breeding, say, a Great Dane with a Chihuahua, they are considered the same 'species'.
Then there are cases where two groups of critters do not mate, even though they are genetically compatable and share the same environment. I believe there was a recent article on a species of butterly or moth that was exhibiting such behavior... would these be the same species even though they want nothing to do with eachother?
The definition of 'species' is really damn arbitrary...
=Smidge=
Not true species, is the only testable (ie scientific, ie non-arbitrary) classification. All the rest are arbitrary. A species is defined as a population of organisms which have reproductive isolating mechanisms which prevent the production of a viable (including sexual) offspring. ie two organisms are members of a different species when they are unable to reproduce and/or produce a viable offspring.
MOD PARENT UP (insightful, informative, underrated)
BSE/CJD don't need any more help...
They looked at 100 proteins to learn what the simple rules are. That does not preclude the existence of rules that are simple. GP was right, if simple rules exist (no matter how we learned what they are), then it is more likely that proteins could arrise by chance, than if the simplest rules for making proteins are complex.
Censorship is telling a man he can't have a steak just because a baby can't chew it. --Mark Twain
I dunno, GP might be right. The fact that a Scientist *can* drop a rock and have it hit the ground, probably means that rocks *cannot* fall off mountains without the aid of some Intelligent Dropper.
Censorship is telling a man he can't have a steak just because a baby can't chew it. --Mark Twain
"This tells us nothing that isn't already known. Of COURSE proteins with related functions share specific patterns of amino acid selection rules or they wouldn't work""
This cannot be assumed; while logical on the surface, that's like saying that porpoises and sharks must be from the same family because they both swim in the ocean and have the same body shape. The scientific method DEMANDS that a hypothesis like that is tested.
"He sounds like he's talking to a little kid. "
In terms of protein chemistry, he probably is talking to to little kids. This article is basically a publicity press release, and is not intended for the scientific community -- their papers in Nature are intended for the scientific community.
and how did it do this?
While you're at it, why don't you ask that any articles about scientific research include the entirety of the published paper(s)? What is important to the casual reader (which is the intended audience) is not the how, but the what and the why.
"One can only assume that these guys chose proteins that don't undergo post-translational modification."
No, one can't assume that. One must read their published papers before leaping to conclusions. Think a bit: if the DNA was expressed in the bacteria, could the proteins not undergo the same post-translational modification as naturally occurring proteins? The research conducted did not test to see what happened during expression, it just tested the form and functionality of the end result, as far as I can tell FTA.
You shouldn't get all worked up because an article intended for the general public isn't detailed enough for you. Many people wouldn't even bother to read TFA (even if they could understand it) if it was written in anything other than plain english.
Someone like you, who wants better information (which is a good thing) should go down to the library at the end of the month and read the published papers in Nature.
"Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
"If there are simple 'rules' to create proteins, maybe that's how nature was able to come up with life so quickly."
Well, first it is sometimes easier to reverse engineer than create. Second, it is also possible to use these 'rules' to support intelligent design. I mean, if "God" were to create life and all that, wouldn't he create an easy-to-replicate manufacturing process?
What those who want activist courts fear is rule by the people.
I'm not sure how simple the rules are has anything to do with the chance that a particular thing arises. A simple rule could be "A standard earth protein must have 37 XYZ chains" - short, sweet, and simple. But how does now knowing that there must be 37 XYZ chains to get a standard protein now mean that before it was known it was simple? Especially when there are more potential combinations than there are atoms in the universe.
I stick by my earlier assertion that simple rules are only simple after they are discovered, not before when the future is unknown, and there are an incredible number of possibilities.
Creationists also like to argue that no true value comes out of studying evolution and that it is proven to be false and ignore the fact that the basic principles of evolution play an enormous role in helping us further understand biochemistry and molecular biology.
I've been on enbrel for six months now to treat my psoriasis (think lizard man from lepar island, not just crusty elbows). It's a protein that I have to inject twice a week since taking it orally would end with my body digesting the meds. I could see genetically engineering a bacteria that could live in the intestine and produce the medicine. That would be awesome.
Disconnect your television. Do your own research. Draw your own conclusions. They're probably lying. Don't be a sheep.
Actually what this supports is the rather obvious but profound fact that evolution happens on many levels. Not only are DNA changes that directly support the individual beneficial, but so are changes that support more rapid evolution. If encoding for proteins has evolved into a simple scheme so that changes generate a higher proportion of fucntioning proteins, then evolution is speeded up.
This is why creationist arguments fall flat on their face - because they don't argue against evolution as theory posits that it will occur but rather against their own simplistic and deliberately implausible (or else impossibly naieve) straw men. In this case creationists might put up the straw man that proteins are too complex to have evolved in the time that the evidence indicates they have, while the reality of evolutionary theory is that, as this research proves, encoding mechanisms themselves evolve, and so on up. The only rule of evolution is this: success breeds success. Success in rate of adaption is as important as anything.
"Even if the relationship between sequence and structure were simple and known (and it isn't, yet), you still have the issue of relating structure to function.
Which isn't known. And of course, even knowing the structure and function of a single protein doesn't mean you know what it's going to do in a complicated environment such as a cell, where there are thousands of things to interact with.
It's a step forward, nonetheless."
Things are not "simple and elegant" in the way you believe.
Evolution is a fact. Darwinism is a joke.
Evolution is both incremental, but also quasi-static due to being driven by the environment. Genetic change builds up in a population over time giving rise to minor varieties none of which likely have an overwhelming advantange. At some point the environment changes - a famine, the arrival of a competitor, a change in temperature, etc, and now in an instant the advantage/disadvantage of these previously benign accumulated varieties/changes becomes apparant, and the evolutionary record shows the population "suddenly" changing. It may well be that a bunch of changes had to occur to arrive at some net change that was beneficial or detrimental, but the point is that these individual steps don't have to themselves confer any advantage/disadvantage - change happens all the time (it's unavoidable) and is undirected (also unavoidable), so you specifically would not expect changes to have any advantage/benefit. It's only when the competetive landscape changes - an environmental change - that these accumulated changes are "put to the test", and maybe evolution will "take a step" as accumulated changes that have advantage/disadvantage in competition and breeding in the new environment play out.
That is why the ID "method" misses the reality of evolution - it assumes that any complex feature was an all or nothing proposition and therefore derives these bogus "feasability" statistics of whether such a set of corrdinated changes could have simulataneously occured. Still, if it makes creationists feel better about their beliefes to "prove" them by ignoring the reality of evolution then so be it. It doesn't change the reality.
Since protein engineering is my field of study, for the benefit of the /. crowd (and my karma) I'll fill in the gaping holes left in the New Scientist article, and give you a little more background on the Nature paper. Because the writeup on /. is a perfect example of "scientific telephone": a semi-interesting result gets written up into a paper, which once it's been through several layers of editors suddenly seems like a major breakthrough.
The Nature paper isn't a breakthrough. It's not even really a major advance. Scientists in my field have been creating artificial proteins for five to ten years now. And yes, even some of them designed completely from scratch (though they're really simple; nothing as complex as, say, ATP synthase) instead of just taking a known fold pattern, known as a "motif." The "WW domain" (domain, in protein parlance, is a small, independent structure within a much larger protein---think of it like a module within the kernel or Apache) is a common fold in hundreds of different proteins. Basically, they analyzed the sequences of all of these WW domains, and figured out which positions were meaningful. It's kinda like reading through some code in a programming language you don't know, and figuring out which lines are comments and which lines are actual compilable code. This group found that the number of interesting positions is small, that they could identify them just from the amino acide sequence instead of having to mess with the whole complicated 3D structure of the domain, and that if they put together a protein with the meaningful amino acids intact and the non-meaningful positions randomized, then in many cases they could still get a pretty decent protein (in terms of structural similarity to the "natural" protein) out of it. Most of the paper is devoted to showing via various methods that they did get a pretty decent protein.
So what does this mean for me, assuming that this paper is absolutely correct (which I admit is a little hard for me to determine with one quick reading, given that I'm just a first-year grad student)? It means that the number of meaningful amino acids in a protein (at least in terms of overall structure) is pretty low, and that they can be identified without knowing what the full 3D structure is. This is good, because for a lot of proteins, the 3D structure is difficult to get. However, they picked an easy target: a small domain where there are over 100 unique sequences known. We'll see how well this method holds up with longer domains and fewer unique sequences. The S/N ratio won't be nearly as good.
Actually, if you can get beyond the "creationist" name-calling, you can see that many Darwin critics are fully on board with common descent, and even natural selection - they just see that there is more to evolution than a pure random process. Micheal Denton, in particular, in his book "Nature's Destiny" talks about stuff exactly like this - that the laws of nature are set up so that are "forms" in nature - that is, proteins and the larger structures they build tend to naturally fall together in certain ways. In this view, the history of life, up to and including huamn beings, was "built in" from the beginning, rather than being the result of a pure contingent process.
There is simply no way to statistically "prove" or "disprove" evolutionary theory. It's not a matter of simple mathematics. You can't quantify all of the variables properly.
I am scientifically inaccurate.
Most creationists are really closed-minded and have an automatic rejection of science. I don't entirely agree with their views.
I think that a lot of these people just assume that since God did certain things, it means that we can never understand them. A lot of them say these things without any basis or anything to backup their claims.
The real breakthru here is reverse-engineering proteins to get their "designer genes". That's one of the goals of giant computational undertakings like Folding@Home. Now every Folding team will be getting our discount coupons on the products of that "free" research we did for the drug companies, right?
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make install -not war
The real misconception of evolution is that it involves random chance to go from nothing to a fully formed species in effectively one-step. This is (as the creationist/ID crowd claims) impossible.
The true method of evolution is an immense form of feedback on a timescale that humans are not naturally able to perceive. Since humans don't live for millions of years it is hard for us to observe and comprehend that very minor random changes in one generation multiplied by billions or trillions of generations can cause massive observed change if you can only look at a couple of those billions of generations.
A simple experiment in genetic algorithms will quickly show how this works.
Start with a random string of bits of the same length as the number of bits used to encode the complete works of Shakespeare (cause you have to use the works of Shakespeare in an example) and then retain those bits that match the pattern and position of one (just one) character in the complete works. With each generation randomize (or mutate) a number of the bits that do not match. After a few hundred generations, you will have if not the complete works of Shakespeare, a close approximation.
"Secrecy is the keystone of all tyranny. Not force, but secrecy
Nooooo, the process he recommended would determine whether it belongs to the species Homo sapien. He didn't say anything about genus.
IF survival of the fittest was true (evolution) then why is there such a biodiversity?
It's not actually survival of the fittest. It is more like "survival of the sufficiently fit".
If you can survive and reproduce, then you have passed the fitness test. Since there are very many ways to survive, there are very many different species that have evolved.
The enemies of Democracy are
...is that it would take such a long time to generate functioning proteins through random chance that it would be statistically impossible
You existing is "statistically impossible", but obviously you are observing you exist as you read this.
Given enough time... Anything is possible, but the most probable thing will happen... Or something... I don't think the human mind can really comprehend what happens in the universe over 10 billion years.
You know what they say about infinite monkeys with infinite amount of typwriters.
"I am the king of the Romans, and am superior to rules of grammar!"
-Sigismund, Holy Roman Emperor (1368-1437)
Your analogy of The Complete Works of Shakespeare is as close to Creationism as I have ever heard (read?) described. Isn't the principle of Creationism or Intelligent Design that there is a goal in in the mind of the Creator and he/it guides his/its creation toward that goal one small step at a time? Wouldn't the very fact that these scientist have found a set of rules simply give us a better insight into the Creators processes and increase our appreciation of the effort and time that has gone into this whole thing we call creation?
The problem with that way of looking at things is that, unfortunately for ID, anything which is statistically improbable can happen by chance, by definition.
"Who is the Journal of Quantum Physics going to believe?" --Stephen Hawking
Creationists are usually not opposed to studying evolution, we're more opposed to Darwinism. Evolution says species change over time, Darwinism says life originated through evolution, and all diversity is created solely through natural selection acting on random mutations. One is a scientifically valid statement. The other is religion.
Many "Darwin critics" are just creationists or anti-science types with religious/nutty objections to evolution. See if they accept what they termed "macroevolution." See if they accept that humans descended from a primate ancestor.
Infinite dead monkeys, since you forgot to feed them?
My apologies for using a contrived example. The only reason I used the complete works is that for a simulation you must specify a goal for testing. If you have a simulation with no specific test that you can see, you'll never know when to stop it or if it's working.
In reality there only test is does this mutation convey a energy, defense, offensive, or reproductive advantage. Meaning that if the members of a species with a mutation have any advantage in producing more young or preventing those without the mutation from producing more young, then they are a success. The part that most do not get, is the size of the advantage required. A mutation that gives a 0.0000000000000001 percent advantage (or less) over other members of that species, will after trillions or more generations allow the mutated members to either dominate or be the sole representatives of that species.
"Secrecy is the keystone of all tyranny. Not force, but secrecy
Phyiscal law and environment obviously constrain what the mechanics of competition & evolution will create, but only in very broad strokes. I don't think you can say, for example, that a carbon-based biochemistry and Earth's environment meant that apes were bound to evolve. Perhaps we can say that the evolutionary/competetive niche of a highly adaptive intelligent non-specialist was bound to eventually get filled, but even that may be over stepping the bounds of speculation.
Anyway, given that the laws of nature can currently be reduced to two (quantum and relativity), soon to be reduced to one, it seems rather unuseful to take this view. If you want to say that God (with supreme foresight, knowing what it would give rise to) designed Shroedringer's wave equation and has then been hands-off ever since allowing the laws of nature to take their effect, then really that makes God rather impotent - entirely powerless to affect your life in any way.
Okay, but in this type of protein research you assume that humans, monkeys, cows, fish, and bacteria share a common ancestor, not merely looking at how a single species changes over time. Creationists usually draw the line when you say that we share a common ancestor with chimps.
Hopefully noone comes up with the biological equivalent of Ice-9...
"Creativity is allowing ones self to make mistakes. Art is knowing which ones to keep" - Scott Adams
This has been provided for. Creationists never believe scientists about the monkeys.
Socialism: a lie told by totalitarians and believed by fools.
Scientists don't use evolution because they're out to win some sort of ideological battle. They use it because it works. They want to understand how an amino acid becomes a protein. Evolution helps explain the process. Creationism and ID don't explain the process at all. They just say two things: (a) god made them; and (b) stop asking questions.
If evolution didn't help further science, it would be abandoned in favor of whatever did. But it works, which is why scientists rely on it and why teachers need to explain it in science classrooms.
Let's hope they figure out with complete certainty what the rules are for making prions -- and then nobody does it.
5 144.300
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Otherwise we've got an Ice-9 problem.
I hope the folks making artificial proteins have thought long and hard about proteins that make themselves -- and what defines them. Meanwhile don't lick your fingers, kids.
http://www.newscientist.com/channel/health/mg1872
'Mad ewes' give birth to BSE lambs
* 27 August 2005
* Debora MacKenzie
* New Scientist Magazine issue 2514
QUOTE
New evidence from an experimental flock raises the possibility that the disease may have spread among Europe's sheep populations.
Sheep develop a disease similar to BSE (mad cow disease) if they eat infected cattle tissue. Now Sue Bellworthy and colleagues at the UK's Veterinary Laboratories Agency (VLA) have shown that BSE can also be inherited in sheep. They report that two ewes experimentally infected with BSE in 2000 gave birth to lambs in 2003 that died of BSE this year (The Veterinary Record, vol 157, p 206). It is the first confirmation of "vertical" transmission from mother to lamb before or during birth - something suspected but never proved in cattle.
Feeding cattle remains to sheep was banned in the European Union in 1994, and any sheep infected that way should have died by now. But the new finding means that BSE could have passed
END QUOTE
I'm curious.... Do you believe in God? Do your beliefs in science stretch back to the fact that the big bang could have occurred by chance? And from what matter? Where did the matter come from? Sorry to get off the subject but I am just curious.
Personally I don't go in for the Christian religion, but you should realize that your question can always be asked. Each time science comes up with a pretty good explanation, and that's all the big bang is, a pretty good explanation, you'll always be able to ask, what was before that. When you ask such a question, you're starting to think like a scientist. But every time you answer the question, you can ask, "Well, where did that come from?", and you can try to come up with good theories up to the point where you start saying "God made it". That's giving up. And where did God come from anyways?
Get real. It sounds just like the "simple, single cell".
No - I don't beleieve in God.
You seem to be suggesting that in seeking the scientific origins of the universe we may at some point get into an infinite regress, but I doubt that will happen. The universe is theorized to have emerged from an expansion event whereby a transiently existant piece of space-time (in the same way that particles can appear out of nothing in a vaccum - in accordance with quantum theory) became permanent. The question then isn't really what was it created out of, but rather where did the dyanamics/rules that gave rise to it come from, and I expect that we'll eventually discover some fundamental rules which are inevitable in the sense of being the only solution to some set of prior possibilities, and thus end the regress (at least in terms of asking why is it *this* way as opposed to "why is it at all"!).
+5 Funny just isn't enough for such a great comment.