Irreducible Complexity

[Saviourmachine]

My question is one of plausibility. Mutations are the only mechanism evolution can rely on to add new genetic information to the gene pool. It is my contention that:

 

Mutations are scarce.

The ones that do occur are usually, to the tune of about 99%, neutral.

Of the remaining 1%, most are harmful.

The ones that seem to be beneficial are very difficult to identify as such.

 

The supposed engine of change is then, not powerful at all. Certainly not dynamic enough to account for millions of species.

Hi txviper, time doesn't matter to me. I have all the time of my life. Mutations are scarce, you are right. The mutation rate must be so low that natural selection can keep it up without decreasing continuously the size of the population. So there is an upper limit. And when somebody say, that mutations aren't rare, that's almost as banal as saying that they are rare. Look, it's very simple to deny statements. It's very difficult to suggest other proposals that can be proved or disproved regardless of the ones that are in direct or indirect contradiction. To prove you're point, it's possible to write computer applications/simulations. That application would have the function to find the appropriate mutation rate to make evolution theory work. Or - a bit more sceptical - what is the upper limit and lower limit to the mutation rate. If the upper limit in regard to some phenomena is lower than the lower limit in regard to some other phenomena you've a sound scientific basis to base your critique upon.

Man! If you gave me two numbers up to 1000 and I had to multiply or divide them out top of my head I want crumble and fall. Likewise with small probabilities multiplied by millions of years. I can't calculate that so fast as you seem to do, that it can't account for the current amount of species. What would the right amount of current different be? A dozen?

 

This is apparent from a (quite random) text like this (source: Computational method to reduce the search space for directed protein evolution [Voigt])

The probability that any single random mutation improves a property is small, and the probability of improvement decreases rapidly when multiple simultaneous mutations are made.

So, scientists are aware of that. By the way, that study handles directed evolution. By iterating random mutagenesis and screening (selection) improvements to proteins are found. I guess you will find this article very interesting because it shows what tricks scientists have to apply to let "directed evolution" work. It's about restricting the search space in the protein fitness landscape. When investigators mutagenize a whole gene, the probabilities mentioned in the quote will decrease even more. Just to be sure, the authors wrote the quote above in this context (entire mutagenization in an artifical environment). Take a look what they say about coupled residues.

 

You all: txViper, Crazy Tiger, Neil, Penny. It's slightly more difficult than saying that the mutation rate is high or low enough. I would appreciate it when you could sustain some of these comments with some data. Don't take me wrong. Difficulties in establishing molecular clock rates are no reason to give up biological evolution. (Or the other way around for txViper.) It does have many pillars (evo-devo is nice isn't it?) and ignorance about theory is no problem for me. I don't know much either.

[Samurai Tailor]

My question is one of plausibility. Mutations are the only mechanism evolution can rely on to add new genetic information to the gene pool. It is my contention that:

 

Mutations are scarce.

The ones that do occur are usually, to the tune of about 99%, neutral.

Of the remaining 1%, most are harmful.

The ones that seem to be beneficial are very difficult to identify as such.

I do not know if your statistics are correct, but even so, the bulk of deleterious mutations are lethal, leading to massive cell death in utero.

 

Beneficial mutations are classed as such based on the selective environment. An example is the beta-globin mutation that, in homozygotes, leads to sickle cell disease. In heterozygotes, however, it provides substantial resistance to malaria without major red cell dysfunction.

The supposed engine of change is then, not powerful at all. Certainly not dynamic enough to account for millions of species.

Says you. The most important aspects are not the mutations themselves but the selection strategies.

Perhaps, though listing these, especially ones with no coincidental deleterious effects, is extremely difficult. Also, it is the “sometimes” in your statement that is the problem. Evolutionary theory is resting on a ridiculously rare “sometimes” device to supposedly push organisms from single-celled ones all the way to outrageous complexity,

I think you need to provide hard numbers before blithely declaring that beneficial mutations are "ridiculously rare."

Adaptation, selection and environmental pressure are not involved here. They are about what happens after mutations supposedly occur. I want mutations to be considered independently.

Er, no. At least, not unless you wish to be accused of arguing against a strawman of evolutionary theory.

Haldane’a dilemma remains a dilemma. It was never suitably addressed, just ignored.

Not so. The dilemma erroneously treated mutation fixations as independent events, such that selection may operate to fix but one mutation at a time. Any biology student can explain why that assumption is incorrect.

The problem with the hidden benefits is that they seem to be so very small that they can’t be documented. To accept that they are there is a position of faith.

Says you. It has been compellingly argued that consciousness itself is a "hidden benefit" of language.

It is an interesting commentary that a new Darwinism had to be formulated at all. In my view, this amounts to two things. First it is a not-so-candid admission of lack of evidence. Second is that I see this as a pivot point where a failing scientific theory rolled over into scientism, a religious undertaking.

You really need to deepen your understanding of evolutionary theory. "Neo-Darwinism" is also known as the modern synthesis - a name given to the period when Mendelian genetics was rediscovered and usurped by evolutionary theory... in the 1930s.

[MrSpooky]

Sweet god, who cares how many negative mutations there are compared to positive ones? As stated before, natural selection will remove the outright negative ones from the gene pool or at least keep em at a very low level.

 

You continue to utterly miss the point, viper. There are two basic points at which a gene can exist... BEFORE the resulting phenotype is affected by the environment, and AFTER it is affected by the environment. Yes, it is true as you point out that upon generation, before the mutation encounters the environment, there are very very few beneficial mutations, a horde of neutral ones, and quite a few negative ones.

 

But it is the point AFTER the genetic phenotype is affected by the environment that you are utterly ignoring.

[Saviourmachine]

Sweet god, who cares how many negative mutations there are compared to positive ones? As stated before, natural selection will remove the outright negative ones from the gene pool or at least keep em at a very low level.

In case I am that sweet god you're talking about. It's not my assertion. But it's certainly the case that the mutation rate as a whole does have a ceiling. Natural selection should be able to weed it out. Like in this article stated:

However, as described in molecular evolution theories applied to theoretical genome populations, the mutation rate has an upper limit set by the requirement of accurate transmission of the genetic information [...]. When this threshold is crossed, disorganization of the mutant distribution of the quasispecies occurs, the genetic information is lost, and the population becomes extinct because of genetic meltdown. This phenomenon is known as error catastrophe.

 

Says you. It has been compellingly argued that consciousness itself is a "hidden benefit" of language.

Maybe interesting for another thread!? Was it a linguist that designed that theory?

[Samurai Tailor]

Says you. It has been compellingly argued that consciousness itself is a "hidden benefit" of language.

Maybe interesting for another thread!? Was it a linguist that designed that theory?

Maybe. Sounds like something Chomsky would devise. I encountered it in Nature via Nurture by Matt Ridley.

[Saviourmachine]

Haldane’a dilemma remains a dilemma. It was never suitably addressed, just ignored.

In case you think I'm ignoring you. That's partly true. Statements like this prove that you even didn't bother to read the headlines of the articles I provided. The Haldane's Dillema is handled in a clear manner by Robert Williams in Haldane's Dilemma. It's not a scientific paper and in layman terms, so you should be able to read it.

It does address that Haldane:

• suggested a deteriorating environment;
  
• considered the 3% difference between chimp and human as attributing to his problem (while of that difference there is only another small percentage beneficial);
  
• didn't account for a subsequent mutation until a mutation had spread over whole the population in the 30 generations he calculated (like dropping a drop of water on a water surface and only allow for a new drop when the surface is totally "wrinkleless" [Google result count 666]).
  

[Kuroikaze]

 

“Neo-Darwinism

Is it so that mutations only add variation to the gene pool?”

 

It is an interesting commentary that a new Darwinism had to be formulated at all. In my view, this amounts to two things. First it is a not-so-candid admission of lack of evidence. Second is that I see this as a pivot point where a failing scientific theory rolled over into scientism, a religious undertaking.

 

“But would it not give evolutionary benefit when certain mutations can be filtered out and others be encouraged?”

 

Of course, This, however is about selection again.

 

“For example, if it's better to double a genetic fragment and only subsequently allow for point mutation, would that genetic system not exist in most modern species?”

 

Doubling a genetic fragment does not mean adding beneficial instructions to the genome. Marvelous things exist in every modern species. The question is about whether or not accidental copy errors are responsible for them.

 

 

this is a misunderstanding of how science works. Yes modern scientists admit that the therory of evolution, as orginally stated by Darwin is in fact inacturate, this is because science knows more about the world than darwin did. When Dawin first posited his theroy they hadn't even discoverd DNA yet.

 

Look at it this way, we know that gravity exists, before Newton people knew it existed and likely came up with lots of therories about how it worked bassed on the information they could gather with the tools they had at the time. Newton devoloped a therory that worked better than the others...so well that it is still in use today. However it is still posible, though perhaps remotly so, that an even better theory will be found. In fact, Newtons theory has been expanded on and changed as more knowledge has been discovered. For instance Newton had no knowladge of black holes, which have so much mass that the gravitational forces will not even let light escape.

 

When these sorts of things happened, scientists didn't just throw up there hands and say, thats it, gravity is stupid and obviously doesn't exiist. No, they just changed the theory to fit the new data. All Neo-Dawinism is a changing the theory to fit the new data.

[Mr. Neil]

I would like to add that Darwin is not a modern biologist, and while there's some historical significance to remembering Darwin's work, modern biology doesn't owe him any special favors. His work is as falsifiable as anyone else's.

 

No one here is a "Darwinist". Heck, I wouldn't even call myself an "evolutionist". I am merely pro-reality.

 

We're not Darwinists for same reason that none of us are Neutonians or Einsteinists or Divinci-ists. We don't worship scientists from centuries past. We admit when ancient works have been outdated and then move forward. For some reason, that seems to be something creationists can't do.

[Zach]

We're not Darwinists for same reason that none of us are Neutonians or Einsteinists or Divinci-ists. We don't worship scientists from centuries past. We admit when ancient works have been outdated and then move forward. For some reason, that seems to be something creationists can't do.

Excellent point, Neil. I'm always shy around the term "Darwinist," particularly because the term can oh-so-easily be used by Creationists to claim that belief in evolution is the eqivalent of religious faith.

 

Scientists don't worship people. We don't give serious credence to anything besides data. If the data lend themselves to evolutionary theory, then so be it. If not, that's fine too. But if you're going to score any scientific points against any theory, evolution or otherwise, you'd best be prepared to discuss the data.

 

Speaking of which, I'm still patiently waiting to see how txviper can explain how horizontal insertion of retroviruses can yield congruent genomic locations through a random mechanism.

[Penny1]

I apologize for not responding earlier, but I've had a busy week.

 

PROOF OF BENEFICIAL MUTATIONS IN ACTION

 

The following article may be of some interest to you:

 

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?...brk.chapter.643

 

 

For those of you unable (or unwilling) to follow the link, I will reprint part of it here.

 

 

---

 

Who let the dogs out?

a genetic classification of dog breeds

 

Are you surprised that the tiny chihuahua belongs to the same species as the imposing great dane? The domestic dog species (Canis familiaris) includes more than 400 breeds that differ, for example in their appearance (size, coat length, and color) and behavior, (guarding, herding, and hunting).

 

More than 150 breeds are officially recognized by the American Kennel Club, which assigns each breed to one of seven groups or a miscellaneous class, based on the uses for which the breeds were originally developed.

 

In a recent study, Parker et al. studied the genetic relationships among a diverse range of dog breeds. They found that most breeds of dog fall into four groupsthree "modern" categories and one "ancient" group that may date back to antiquity.

 

The modern categories include breeds that have been around for fewer than 400 years:

 

 

Working dogs/guard dogs, e.g., mastiff, bulldog, boxer

 

Herding dogs, e.g., Belgian sheepdog, collie, shetland sheepdog

 

Hunting dogs, e.g., scent hounds, terriers, spaniels, pointers, retrievers

 

 

This genetic classification of breeds grouped dogs together in a way that matched similarities in morphology and geographical origin. However, there were some surprises. For example, the oldest of all dog breeds are commonly believed to be the Pharaoh Hound and Ibizan Hound, which resemble the ancient Egyptian dogs drawn on tomb walls more than 5000 years ago. However, this study failed to detect their ancient lineage. This may be because they are modern recreations of old breeds or because current tools are unable to detect their ancient genes.

 

In contrast, a diverse group of dog breeds appears to be most related to the dog's ancient ancestor, the grey wolf. These breeds include dogs whose appearances resemble the wolf (e.g., the Siberian Husky) and dogs that do not (e.g., the cuddlely Sharpei). Breeds that belong to this ancient grouping are diverse and originate from different continents, e.g., the Afghan from the Middle East, the Basenji from Africa, the Tibetan Terrier from Tibet, the Pekingese from China, and the Alaskan Malamute from the Arctic.

 

Parker et al. looked at microsatellites to find the genetic differences between breeds of domestic dogs. Microsatellites are short segments of DNA that contain repeats of DNA sequence. The repeats usually occur in a noncoding part of the gene, and their number is highly variable. Analysis of the microsatellites of 414 dogs representing 85 different breeds revealed that the degree of genetic differentiation between dog breeds is much higher than that found between human populations on different continents!

 

Given that most modern dog breeds have existed for fewer than 400 years, it is surprising that dog breeds are genetically distinct. But a dog can be matched to its breed by its individual genotype. Of 414 dogs tested, only 4 dogs were assigned to the wrong breed.

 

This apparent genetic isolation of dog breeds through selective breeding was reinforced by the formation of breed clubs in the mid-19th century. Rules such as the "Breed Barrier Rule" states that "no dog may become a registered member of a breed unless its dam and sire are registered members". Such selective breeding generates not only genetically diverse breeds of dog but also leads to the accumulation of mutations and inherited diseases. By using a genetic classification of dog breeds, scientists will be able to select breeds of dogs that share the same ancient mutations and genetic predisposition to diseases that some humans have. Analysis of this DNA is more likely to yield information about the diseases and the mutations responsible for them.

 

---End quotation---

 

 

It's simple: genetic improvement has been hiding under our noses all along. There is no way for human beings to tamper with the genetic sequence of a dog directly, until perhaps a few decades ago. All changes had to be made through selective pressure. The genotypes of these dogs are all different, yet it is observable within recent history that all these breeds of dogs did not formerly exist. We know for a fact that these breeds of dogs did not exist before we began selectively breeding them. We also know that these breeds of dog are genetically different. We also know that these genetic differences account for changes in phenotype (longer legs, improved endurance, smallness or largeness, long, silky coats, short wiry coats, the list goes on and on) which account for the differences. That's an awful lot of beneficial mutations. Yes, there have been some fatalities bred into dogs as a result of our selective pressures, but that is the imperfection of man, not of environment. In another words, if the selective pressures had been those of nature and not of man, those imperfections would have been weeded out--and, there would have been a substantially longer length of time in which to produce hardy offspring with beneficial genotype changes.

 

Dogs have been selected for breeding in such a way that genetically diseased animals are avoided for breeding stock, while those which do not have those diseases present are selected for breeding. This is the same thing which may occur in nature, only the less fit animals would die, and hence, not breed. The individuals free of disease would breed. In this way, fatal mutations induced by the pressures of mutation would be driven out of the population.

 

There you have it: beneficial mutations in dogs.

[crazy-tiger]

Standard Creationist answers...

 

"But they're all still dogs" - ignoring the huge genetic differences, which are not far from being a different species...

 

"That's a form of Intelligent Design" - ignoring the fact that humans didn't design any of this, and that we're nothing more than part of the natural selection process...

 

"Short legs in a swamp is not a beneficial mutation" - ignoring the environment which defines whether something is beneficial or not... (yes, someone has pulled that one out on me before)

 

 

 

Any guesses at which one TX will use?

[Mr. Neil]

"That's a form of Intelligent Design" - ignoring the fact that humans didn't design any of this, and that we're nothing more than part of the natural selection process...

And let's not forget the kid brother of that argument, "That's just artifical selection!" A standard creationist canard.

 

There's really no such thing as artificial selection. We're as much a part of the dog's environment as anything else. The canines have simply adapted to a domestic lifestyle, and those traits unfit for domestic life are weeded out.

 

 

And yet another: "Natural selection has only selected domestic traits that were already there prior to domestication."

 

Even if this is true, it's entirely irrelevent, because CT's argument shows that beneficial mutations happen anyway.

[crazy-tiger]

"That's a form of Intelligent Design" - ignoring the fact that humans didn't design any of this, and that we're nothing more than part of the natural selection process...

And let's not forget the kid brother of that argument, "That's just artifical selection!" A standard creationist canard.

Oh yeah... I forgot that one.

There's really no such thing as artificial selection. We're as much a part of the dog's environment as anything else. The canines have simply adapted to a domestic lifestyle, and those traits unfit for domestic life are weeded out.

Hmm... I suppose you could call it Intelligently Directed Natural Selection.

 

Even though it sounds quite like ID, it's nothing like it because there's no damn design in there... so you Creationists can stop drooling over a new way to slate evolution.

 

 

 

 

 

Oh yes... I could HEAR you drooling over that one...

[Penny1]

 

Hmm... I suppose you could call it Intelligently Directed Natural Selection.

 

Even though it sounds quite like ID, it's nothing like it because there's no damn design in there... so you Creationists can stop drooling over a new way to slate evolution.

 

 

Actually, the selective process, or "design" part, wasn't even important to my argument. All I needed to to do was prove that beneficial mutations could occur while negative mutations are weeded out, and still produce healthy, viable offspring, in a way that could be easily demonstrated.

 

The "Intellegent Design" of human beings did not "engineer" the beneficial mutations that were observed.

 

I think I've made my point.

 

 

"BEHOLD!" sayeth God! "I give you the Chihuahua! Go forth, little dog! Be fruitful and multiply!"

 

And God saw that it was very good indeed.