Ready, Steady, Evolve 911
Stront writes "New Scientist is reporting that plants and animals can 'bottle up' evolution until they need it. A certain protein 'hides away' mutated genes acting like a genetic valet, however in extreme environments, such as high temperature or noxious chemicals, the cleaning process breaks down and the mutations are released all at once. This goes some way to explaining examples that are considered to defy standard evolutionary theory, such as the Bombardier Beetle."
More info please! (Score:3, Informative)
Re:Article? (Score:2, Informative)
Evolution (Score:4, Informative)
Just look at the classic example of ants collection food. It is beautifully described in John R. Koza's [genetic-programming.com] great books (1 [amazon.com], 2 [amazon.com] and 3 [amazon.com]) on the subject.
Just imagine adding a fermone layer to freeciv [freeciv.org] and let the random search for a superior player begin.
Re:Hmm... (Score:2, Informative)
Doesn't this kind of go against the theory of natural selection? I mean, if the mutated gene is hidden, then there really isn't a difference between the inferior and superior versions, so the gene pool won't be improved.
Not really. Suddenly hostile environment would probably kill off a large proportion of the population in a short time (evolutionarily speaking). If any hidden combination of genes expressed themselves then and even slightly affected the odds of survival then the resulting population would be replete with this set of genes.
Bombadier Beetle faq link (Score:5, Informative)
There's no great mystery; all of the chemicals are common, other beetles exist that excrete them separately; and the temperatures and pressures are not really that great (only just above boiling). So what?
Re:Less potent (Score:3, Informative)
There's a good account of such a possible route here [talkorigins.org]
The steps listed are not claimed to be the route, just a possible route.
Re:I have serious doubt. (Score:4, Informative)
No, because there is nothing evolutionarily "bad" about cancer, so long as you don't get it until you've had offspring.
"But we have record in all older human of a superior alien power interfering which life on this planet."
So aliens came and jiggered with life on earth - cool. One then simply wonders... how did this superior alien lifeform come about? Infinite regress...
"You guy defending the evolution theory so keenly are in fact a new kind of religious zealot - you just replaced the trinity with natural sciences.
I wonder when the first fires will burn and the whitchhunts start."
Total sensationalist bullshit. There are many, many excellent popular books on the subject. Why not educate yourself? Or wait for the aliens to take you away...
that darned beetle (Score:3, Informative)
There are many organisms that use what would be lethal chemicals to disorient, disable and/or kill their prey and/or predators. If you think of the squillions of beetles in the world (and there really are billions and billions of them), then look at the amount of time they've existed (a very very long time), is it really that surprising that such a feature could evolve?
Something as advantageous as being able to secrete chemicals that predators don't like gives you such a massive advantage over your defenseless peers that natural selection is going to promote that feature very aggressively, then one beetle arrives that has slightly too powerful secretion methods that squirt the chemical rather than simple secreting it onto their exoskeleton. Now you have an even bigger advantage, you can deter your predator before it has you in it's mouth. Again, natural selection is going to promote that quite aggressively because you're less likely to be injured and unable to reproduce further.
I admit that the leap from there to squirting two different chemicals so they meet at a precise point and react is a little greater, but it only has to happen by random chance once, after that natural selection (less other random chances of death) will take care of making it the predominant feature.
Given the incredible amount of specialisation nature displays elsewhere, the bombadier beetle doesn't seem to be too out of the ordinary. I would suggest that something like bioluminesence is equally impressive/unlikely.
About the word "Theory" (Score:5, Informative)
Another meaning is of governing principles as in "theory of operation". I have a book at home call "Loudspeakers: Theory and Design". The author does not offer hypotheses about how speakers work; he has no doubt as to whether they work and how they work. He's not writing conjecture - he's writing science and engineering - the general body of rules governing the operation of loudspeakers, which the author collectively refers to as their "theory of operation". This second sense of the word can be defied.
In the days of Darwin, the word "theory" in "Theory of Evolution" probably may have refered to the first sense of the word, as a hypothetical explanation of the origin of all species, including ours. But talk to a biologist or naturalist today and he'll tell you they have no doubt but that evolution is a fact; how it works, its principles of operation, is something they're still exploring and trying to explain.
This confusion between the meanings is something the Bible-thumbers love to exploit (I'm not lumping you in with them, though). They jump up and down and shout about how evolution is just a "theory" and that their half-baked Creation Science theories deserve equal consideration in the schools. Don't buy it. Evolution is a fact. We're sure of the big picture; it's just some of the details that we haven't worked out yet.
--Jim
Re:how does one hide a gene? (Score:1, Informative)
Its MOOT, as in MOOT point. MUTE would be your
crippled deaf mother that can't speak.
It's called Punctuated Equilibirum... (Score:5, Informative)
Re:About the word "Theory" (Score:2, Informative)
Evolution also refers to two things, one is a fact, the other a theory.
The idea that life did not suddenly appear fully fledged, but that simpler forms appeared and gradually more complex forms developed from the simple forms is indesputable except by total weirdos.
However, the idea that this evolution was driven simply by random mutations coupled with natural selection *is* just a theory.
I don't know who you mean by "we" when you say "we're sure of the big picture" if you mean that we're sure that this is how it works. I used to believe in the neo darwinist theories [NGT] completely, but two years full time work with genetic algorithms changed by mind. GAs work, but not as well as they would need to for life to have evolved in the time frames involved. It does not add up. GAs work I recommend "Not by Chance" by Dr. Lee Spetner who explains why not in a more authorative manner than I could manage.
Re: "thinking" (Score:5, Informative)
> THIS IS A THEORY! It seems to explain the world in a decent way, but 5/10/25/100 years from now we could find a better one.
Notice the important and not particularly subtle difference between evolution, the theory, and evolution, the phenomena that the theory is intended to explain. Sure, we might find a better theory someday, but the underlying fact that life has evolved enormously over the past several billion years is not going to go away.
> There is so much about our physical world that we don't understand, that I'd say it's likely that evolution is wrong in it's current form.
That's a complete non sequitur. If you s/likely/possible/ then it will pass muster. But even so, scientific theories aren't quite so disposable as some people seem to believe. And even the biggies, such as the generalization of Newtonian physics to modern physics, always move our understanding of the universe further away from the naive mythology of the Bronze Age rather than moving us back toward it.
> For example, the creation of life: our current theory says chemicals and energy came together in a primordial soup and formed basic life.
Sorry, but "the creation of life" is not a part of the phenomena or theory of evolution at all. Evolution happens whether life arose from a "soup", was created by a god or committee of gods, has always existed, was sent back from the future, etc. The theory of evolution makes no claims whatsoever about what caused life to start.
> Is it possible? Sure, I guess, but seems to me the idea of a higher power is just as plausible as the soup.
This is absurd. We know that the ingredients of the soup occur naturally in the universe, and we know that our bodies are merely bags of chemicals, but the existence of a "higher power" is purely speculative. (Notice that I don't rule out the existence of a "higher power"; I merely point out the absurdity of invoking one as an equally plausible explanation of anything.)
>
As I said, we haven't been discarding the major theories at a very high rate, and whenever we do, it never leads us any closer to an Invisible Sky Man as an explanation for anything. If the theory of evolution is ever discarded or substantially revised, you can bet that the result isn't going to be any more pleasing to creationists than the current theory is. And that's because the underlying facts that any theory must explain aren't going to go away.
Re:Hmm... (Score:3, Informative)
Yup!
http://www.talkorigins.org/faqs/bombardier.html
the bombardier beetle evolved just like everything (Score:4, Informative)
A step-by-step evolution of the bombardier system is really not that hard to envision. The scenario below shows a possible step-by-step evolution of the bombardier beetle mechanism from a primitive arthropod.
1.Quinones are produced by epidermal cells for tanning the cuticle. This exists commonly in arthropods. [Dettner, 1987]
2.Some of the quinones don't get used up, but sit on the epidermis, making the arthropod distasteful. (Quinones are used as defensive secretions in a variety of modern arthropods, from beetles to millipedes. [Eisner, 1970])
3.Small invaginations develop in the epidermis between sclerites (plates of cuticle). By wiggling, the insect can squeeze more quinones onto its surface when they're needed.
4.The invaginations deepen. Muscles are moved around slightly, allowing them to help expel the quinones from some of them. (Many ants have glands similar to this near the end of their abdomen. [Holldobler & Wilson, 1990, pp. 233-237])
5.Some invaginations (now reservoirs) become so deep that the others are inconsequential by comparison. Those gradually revert to the original epidermis.
6.In various insects, different defensive chemicals besides quinones appear. (See Eisner, 1970, for a review.) This helps those insects defend against predators which have evolved resistance to quinones. One of the new defensive chemicals is hydroquinone.
7.Cells that secrete the hydroquinones develop in multiple layers over part of the reservoir, allowing more hydroquinones to be produced. Channels between cells allow hydroquinones from all layers to reach the reservoir.
8.The channels become a duct, specialized for transporting the chemicals. The secretory cells withdraw from the reservoir surface, ultimately becoming a separate organ. This stage -- secretory glands connected by ducts to reservoirs -- exists in many beetles. The particular configuration of glands and reservoirs that bombardier beetles have is common to the other beetles in their suborder. [Forsyth, 1970]
9.Muscles adapt which close off the reservoir, thus preventing the chemicals from leaking out when they're not needed.
10.Hydrogen peroxide, which is a common by-product of cellular metabolism, becomes mixed with the hydroquinones. The two react slowly, so a mixture of quinones and hydroquinones gets used for defense.
11.Cells secreting a small amount of catalases and peroxidases appear along the output passage of the reservoir, outside the valve which closes it off from the outside. These ensure that more quinones appear in the defensive secretions. Catalases exist in almost all cells, and peroxidases are also common in plants, animals, and bacteria, so those chemicals needn't be developed from scratch but merely concentrated in one location.
12.More catalases and peroxidases are produced, so the discharge is warmer and is expelled faster by the oxygen generated by the reaction.
13.The walls of that part of the output passage become firmer, allowing them to better withstand the heat and pressure generated by the reaction.
14.Still more catalases and peroxidases are produced, and the walls toughen and shape into a reaction chamber. Gradually they become the mechanism of today's bombardier beetles.
15.The tip of the beetle's abdomen becomes somewhat elongated and more flexible, allowing the beetle to aim its discharge in various directions.
Re: About the word "Theory" (Score:4, Informative)
> I used to believe in the neo darwinist theories [NGT] completely, but two years full time work with genetic algorithms changed by mind. GAs work, but not as well as they would need to for life to have evolved in the time frames involved. It does not add up.
GAs, as usually implemented, are a very bad model for biological evolution. That's because they aren't intended to be models for biological evolution; they're merely inspired by biological evolution.
However, they are useful for demonstrating some principles that creationists are fond of denying. Such as the fact that completely random mutations in the genotype, when filtered by a biased selection process, can result in evolutionary "progress". They can also show the importance of the component processes, e.g. take your favorite GA and run it with mutations turned off and see what happens, or run it with random selection rather than fitness selection and see what happens. You will find that GAs make a very good case that random mutations filtered by natural selection are a plausible explanation for change in an otherwise unguided system, such as the earth's biological system.
> I recommend "Not by Chance" by Dr. Lee Spetner who explains why not in a more authorative manner than I could manage.
I have not had time to read Dr. Spetner's book, but I am told by scientists who have read it that he pulls a real whopper of a bait-and-switch argument when it comes to the dénouement. You may want to visit the talk.origins newsgroup and ask about the logic of Dr. Spetner's argument before you take him too strongly to heart. For a warmup, read this [google.com]:
Re:Missing the Point? (Score:3, Informative)
The fact is, the theory of evolution explains perfectly well how something like this beetle could have evolved. There are numerous other beetles, which have the same chemicals, although, use them differently. There are also numerous examples of dangerous "design" in the animal kingdom (Our Windpipe right beside our food-pipe for crying out loud)
There is, as yet, no known species which could not have come into existence through a mechanism like evolution. Therefore, evolution, at present, is an excellent theory.
parahydroxybenzene (Score:5, Informative)
I'm doing the traditional /. thing and not actually reading the article, but I assume it's the old news on heat-shock and chaperone proteins being shown to be a general case.
This isn't "saving up" mutations. This is a system for supressing aberrant mutations breaking down in stressful environments. The True Believers out there would like to phrase this to illustrate the cleverness of natural selection, but this is the failure of a beneficial system leading to a honking buttload of mutants appearing. Nothing more. Yes, throwing a bunch of random solutions at the problem may find an answer and allow a population to continue living in a stressful environment, but it's a bit assuming to try to say the system has evolved to break down in this manner (though it is a rather elegant failure mode).
As for the bombardier beetle...
Hydroquinone and hydrogen peroxide, when mixed, turn brown over the course of a couple minutes and won't taste very good. Various beetles besides the Bombardier Beetle use the chemicals, uncatalyzed, merely for the foul taste. Evolution can work in as many steps as it likes increasing the foulness of the taste without any delightful imagery of exploding beetles occurring to anyone.
Of course the page linked to is slow to abandon such delightful imagery so, while it is kind enough to mention that nothing very exciting happens unless you add a catalyst, it likes to give the impression that without that catalyst (or "anti-inhibitor", if you please) the beetles would die a horrible death in the manner of a piece of popcorn, though not quite as tasty.
Let me let you in on another "secret". There can be huge ranges of activity in classes of closely related proteins. This is especially true of the enzymes responsible for catalyzing naturally occuring reactions between simple chemicals. This is a bit of a problem for the Creationist because their idea of the beetles stumbling across a highly efficient enzyme and blowing themselves to bits for generations is very useful. Having them stumble across a weak version that merely made them taste a little worse than their competitors when an attacker mixed the chemicals together is hardly an exciting idea. Nor is it exciting for this weak enzyme to follow the same path of increasing the foulness of the taste that the parahydroxybenzene glands went through.
Of course, once this enzyme reaches a certain level it does get to be dangerous to the beetles. Chance encounters with learning predators that may have only have caused injury become fatal due to the beetles' own defense mechanism (though, because the added foulness of taste deters predation, this is still beneficial to the species, though not to the individual). Any solution is beneficial, as the alternative is death. The apparent winner is to excrete the chemicals, which isn't surprising as some of the other Brachinus species do this without the fun of superheating. Coevolution of improvements to the catalyst and to the ejection system gives us what we have today.
Unfortunately, answering one set of Creationists' call to provide an explanation is met with catcalls of "just-so-story!" from another set. It's really best to ignore them as a group... which, hey, is what I'll be doing.
Random Comments on Biology and Slashdot (Score:5, Informative)
I have an MS in ecology and population genetics, but have also made my living in the CS field for years (to pay the mortgage, you understand
Evolution (and I've taught college courses on the subject) is not engineering. To understand it, you need to understand ecology, genetics, biochemistry, lots of general biology, etc., etc. There are few topics with more misunderstandings, by people who think they understand it all, and don't. Including some people in the field, har har.
Finally, regarding the Creationists and the "irreducible complexity" thing. As the Theory of Evolution got traction in the intellectual world, the Creationists always pointed out something we didn't understand as proof of a Creator. As more and more became understood, they retreated to the next thing. This was called the "God of the gaps" approach - if we don't understand NOW what's going on, it must be GOD!
That's how I feel about "irreducible complexity". It will be found to be reducible. Well, maybe, mabye not. Where is it written that talking monkeys should necessarily come to understand the Cosmos in all its glory? That's what we are, boys and girls. For all our wonderful accumulated knowledge, there's an infinite ocean of subtlety out there... there's no guarantee that it's all accessible to our brand of cognition or any other computation either.
We return you now to your regularly scheduled trollfest...
Re:Why can't we think for ourselves? (Score:2, Informative)
Re:Bombadier Beetle faq link (Score:2, Informative)
Re:Random Comments on Biology and Slashdot (Score:2, Informative)
Actually the concept of irreducible complexity is described as follows
An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.
To me this sounds simply to be a quantification of the likelyhood of a mutation to arise. In particular a series of non-beneficial mutations that are at the end beneficial. The mechanism above for "storing" a series of mutations seems a pretty good example of a way to bypass the non-beneficial steps to get to the benefit of the combined mutations. The only barrier then is the probabilty of such mutations being a beneficial combination. Just because the idea for measuring complexity comes from creationist research why does it need to be 'debunked'. If the definition of the term is usefull why not just use it?