Cells do not "transform" into complex organisms. Via endless rounds of natural selection, genotypic modification and selection gives rise to incremental phenotypic modifications and divergent lineages. As for evolution, it is an "interesting theory" since a "theory" is a body of scientific explanations for phenomenon supported by testable predictions and evidence. No doubt the word you meant to use was "hypothesis". Evolution, fitting all of our testable predictions in the same manner as any other well-founded theory would, is on no worse epistemological ground than cell theory or atomic theory.

Forgive me for not writing "group" of cells.

Forgive me for using a synonym for "hypothesis" instead of "hypothesis" itself. If you want to waste time with unneccessary technical definitions of the words I used in my question how will we actually address the point?

Also forgive me for asking if you intentionally threw a pile of words at me that really weren't needed?

And evolution isn't in any way as simple as cell theory and atomic theory, nor surely is it as observable due to the relatively vast time window.

Ali

Hey, thanks for the response.

How is pharmacology based on evolution?

And how is it the foundation of all modern biological science?

I was using "theory" in a more conversational way than the precise scientific definition, I apologise for any confusion I caused.

Ok, its fine you saying that there "isn't any doubt in the legitimate bio.." but let's not let that take away from our own thinking...

Just out of interest do people see any faults in Evolutionary theory?

Great... We are already arguing and I've only just started the thread.

Sorry if I am not wording my posts very correctly or friendlily - I'm lying half asleep in bed (2:40am in this nice non-america).

I will point out that I didn't say that you said it was simple - it was merely one of the points I mentioned to try and describe my doubt that they are similar in their evidencial strength. Our testible predictions are, once again, surely on a very small time frame in relation to the concept of evolution itself - I know its the best proof that we can provide of it but, compared to eg cell development your ability to truely test the theory is a lot more limited.

I know you were just trying to help by giving me the definition but I didn't ask for it (that's why I thought it was unneccessary)... plus you could have put it in much simpler terms for us 'lesser' people to understand.

What straw man did I make?

My apologies. I just got somewhat irked by your misunderstanding of what the words "evolution" and "theory" mean. You can't understand how frustrating it is unless you deal on a regular basis with people who make a living confusing other people about evolution.

When I first read the thing about plasmodium falciparum I thought it was a pretty interesting one, picturing a more physical  tube/valve development but it seems to be more of a chemical setup - more of an inter-cellular drug/metabolite transporter? I know, again with time frames, it may be hard for us to observe anything more physical but are there any examples of physical development?

I see how it could be the most connected of the disciplines but for, just a random example, DNA replication science surely isn't 'based' on evolution theory as such. I understand that it could be connected to it though, but connections such as that surely wouldn't be classed as foundational.

Thanks, and I can understand that you would get annoyed at it. I'm not going to claim that I'm in any way a biologist (I study engineering so some would even have trouble calling me a scientist) but I reckon it never hurts to ask questions.

The case I was referring to was the development of a new ABC-transporter. ABC transporters are part of a superfamily of P-type ATPase pumps. This particular pump allowed the pathogen to become resistant to chloroquine by pumping it out of the cytoplasm. This was an evolutionary change brought on by natural selection of the malarial parasite in response to the employment of chloroquine as a drug to treat malaria. It's evolution was the result of a duplication, an event where a superfluous copy of a gene is created. This allows one or the other copy to be selected for a role different to that of its sister. This is called a paralogy.

You misunderstand what I mean. It is possible to study specific biological subjects, such as the mechanisms of a replisome, as you mentioned, outside the context of evolution. However, it is not possible to have a meaningful or coherent understanding of biology without evolution, because evolution is the unifying theory of biology. In the same way as it is possible to study both quantum mechanics and relativity in the context of the fact that no unifying principle exists between them, but this produces a disjointed understanding. WIth respect to biology, evolution is the unifying principle. As previously mentioned, it allows all disciplines to be unified and without it, no understanding of biology could be even remotely complete. It is the foundation of biology in the sense that everything in biology refers back to it. 

I think he means things like genetic drift, gene-hopping, selection pressure, population dispersion, and so on -- the mechanisms by which genotypes change and diverge.

That sounds like what I meant, although I'm not even going to pretend to know what all of them mean/ how they worked.

OH, for Fuck's Sake!  If you're going to spam the board with pages of HUGE FONTS and linked texts, at least have the decency to pick texts that have PARAGRAPHS instead of long run-on sentences.

Go live under the bridge, troll.

-HD

I'm not making any friends here it seems... aren't I great at first impressions? I know it is pretty ignorant me not reading what you linked to, and I am sorry if I sounded dismissive but it is a lot of content and I haven't got a lot of time to be on here so I just don't have time to read it.

Also it did seem that you provided your own summary of what it was saying, which is what I based the  "biology being dependant on sex" statement on. 

It's also not a good practice for me to be telling you you are wrong in the last post but hopefully you will agree that I wasn't as much in the wrong as it was made out.

And I'm sure if that essay was inexistant you would find a way pf communicating your points to me so that way I might still "have a clue" what you are talking about.

But I still think there is a more distinct difference between chemical imbalances due to cell mutations and the development of more complex systems such as an eye

"Chemical imbalance", "cell mutation"? These are meaningless terms. The case I refer to is the generation of a novel P-type ATPase due to selection pressure of the use of the drug chloroquine. Cells do not "mutate". DNA, the central hereditary molecule of biological life (Deoxyribonucleic acid), is what changes on the basis of random mutations to which selection pressures are applied.

The principle upon which a novel P-type ATPase is generated in response to the employment of chloroquine is identical to the processes which generate more complex biological structures such as the eye. In multicellular organisms, because there is a more complex pattern of what is referred to as combinatorial control, there is greater opportunity for innovation. It's funny that you mention the eye since this serves as one such example. I can go through some basics of the evolutionary biology behind the generation of novel structures in multicellular organisms.

One striking result of combinatorial control and AP [anterior-posterior axis] gradients is that a  single GRP [Gene regulatory protein] can initiate the transcription of multiple proteins. Even more striking is the suggestion that it might be able to initiate the formation of an entire organ. One example of this is the protein called Ey, called eyeless, which triggers a battery of genes responsible for eye development. This was strikingly demonstrated when it was transiently activated in a cell line destined to form the leg of the Drosophila. The researchers found a perfectly formed Drosophila eye growing on the leg of the fly.

Obviously in this description some terms must be clarified. An AP gradient refers to the gradient of concentrations of distinct GRP (gene regulatory proteins) within certain sections of an embryonic precursor called a syncytium. It is formed by a large group of nuclei in a common cytoplasm. A cascade of GRP operate on different concetrations depending on their position along the AP, giving rise to distinct transcriptomes [expression patterns] along the cell. This is the precursor to embryonic development. These tend to be arranged in "stripes" which can be switched around by substituting the GRP-motif on one gene for another, which gives effects like this one below:

Ultimately, the point to take away is that the genomes of multicellular Eukaryota are made up of many distinct modules of genes, with their distinct regulatory regions and offerings for combinatorial control. The arrangement, sequence, and position of these modules, along with the intron divisions along a sequence, allows for modular innvoations and reshufflings, creating new and novel combinations of proteins, expression patterns, and biological structures. This principle can be extended from understanding how, for example a new protein might form via homology and recombination, to, for example, how the generation of a novel expression pattern might generate a new biological structure, or refine a previous one.

Plus, how does the development of an eye (for example) agree with evolution through natural selection?

You are obviously very confused. Prior to this point, we have been discussing the molecular mechanisms which describe the manner in which innovatiosn are generated at the molecular level and are responsible for phenotypic changes. Natural selection is the principle which describes how these innovative changes may be propogated throughout a lineage, since it is the process by which changes in gene frequencies are brought on by selection pressure. Any advantegous phenotypic change will cause a change in gene frequencies over time within a population. This is the basis for the development of complex structures in a gradual process via incremental phenotypic changes. Evolution can be understood broadly as the study of two things: The first is mutation, the generation of innovation and the molecular mechanisms which are the basis of phenotypic changes, which generate variations in a population. The second is selection, which describes how the frequencies of these different variable genes (called alleles) may spread throughout a lineage, hence generating the effect which we call "descent with modification", the change in the appeareance of the members of a lineage over generations.

Gravity is a law though, right? 

So phenomena such as evolution and plate tectonics can never be laws because they take too long to observe, right? 

Pardon my ignorance, I'm a liberal arts student through and through.  Perhaps I would better understand this in haiku form. 

Ok - I don't think I'm going to get the wording right but yes, the "chemical imbalance" meant the protein imbalance/changes and the "cell mutation" meant the DNA alteration that effectively caused it. (It should be pointed out that both terms are still meaningful - though I would say chemical imbalance wasn't quite right in this context- and cell mutation IS a used" phrase, even if it isn't neccessarily 100% accurate).

I know I'm changing my question but I have for most of this thread been trying to angle more at the larger alterations.

Surely an eye, before it works, is no more than a source of infection and weakness and thus will be more detrimental to any creature developing it. As a result, in my ignorant way, it looks like this would conflict with the principle of evolution due to natural selection.

And you (again!!!!) ignored my other points! They probably are stupid like the rest of the posts but you might as well tell me where I'm going wrong.

So (from waaay above) you think unifying is the same as foundational? Or is that just a small part of it?

Also the processes you mentioned (if my attempted understanding of them is correct) surely would throw up a LOT more ineffective/"dead end" organs than effective ones but we don't really see many of these... Do you know why that is?

Surely an eye, before it works, is no more than a source of infection and weakness and thus will be more detrimental to any creature developing it.

This is a fallacious argument. As a fallacious argument, it is often referred to as "irreducible complexity". The argument largely rests on ignorance of the processes by which biological structures are generated under natural selection. We have established, firstly, that the proteins are homologous and hence arose by means of duplication and divergence. The argument you make states that biological structures only have advantages as finished products and are deleterious prior to that. This is fallacious because the manner in which biological structures are formed under mutations and descent with modification does not work like "part adding". Evolution is not an assembly line being directed towards a finished product. For example, When homologous duplication takes place, a not so uncommon phenomenon is called double-deleterious incapacitation, that is if the homologous copy does not form a psuedogene, then often, since neither is being heavily conserved by virtue of the fact that a copy can assume the function in question, if a homologous gene had multiple functions such as if it is a gene command locus, then if both copies suffer a deleterious mutation that forces certain functions of the locus into incapacitation, then suddenly both copies are conserved, and so the homologous gene is propogated and cannot become a psuedogene. A molecular biologist who was naive might conclude that the system was "irreducible" by virtue of the fact that both parts are required, but homologous duplication contributes the bulk of evolutionary novelty, and such irreducibility is an illusion because the system was never working towards the current system in the first place.We should understand this in the context of duplicative divergence in the context in

The recombination of genetic material can extend far above the level of single proteins or domains. Indeed, enormous chunks of genetic material may be recombined. Hence, when examining homologies, we can examine relationships that go up to the quaternary level, caused by large order duplications or recombination. Indeed, we are often tempted to think of evolutionary increment as “adding parts” or something of that like. This is a very primitive design-style worldview of looking at evolution. Indeed, the process can add parts and delete parts via these mechanisms, but this is a rare occurrence (begging the question of what a single “part” is anyway). Many complex biomolecular structures can generated by the recombination of pre-existing structures into a new role, which is a rapid-order mutation, instead of incrementation to generate the whole structure in question, incrementing generates some of the underlying mechanisms of the structure in question, and then these underlying protein structures may recombine to rapidly form the product structure. If only two or three pre-existing major components are required to generate the new and supposedly “irreducible” function, then it can be generated by what is called exaptation which is, as described, a process by which major structures (which may have no relevance per se to the function which they recombine to form) recombine and create something, which, when broken down into its fundamental constituents, appears irreducible. Thus, in your example, you are totally incorrent in stating that the precursor entities towards what we recognize as the eye are deleterious, because organic structures result from the preexisting structures (exaptive mutations). These structures have useful functions under selection in turn, independant of the functioning of an eye. Your argument is based on eschatology. Evolution is not eschatological. There is no "working towards" the eye. There is selection pressure all the way, even if that selection pressure does not pertain to vision.

Hence, we may conclude, that instead of this backward examination (what is the effect on X if we remove a part?), which presupposes an eschatological nature of evolution whereby the system works "towards" this goal by means of "adding parts", we view evolution, not being escathological, as using exaptation to recombine pre-existing functions to create the new mechanism. When we subdivide this not by its functional homologous relationship to other mechanisms, but rather by an arbitrary definition of a "part" is where the fallacy occurs, and the illusion of Irreducibility is generated. With respect to the eye, for example, the original precursors of vision had nothing to do with sight. They originate from light sensitive cells in prokaryota with different functions. The light sensitive proteins that are responsible for the signal transduction that occurs in the optic nerve is a descendant of a protein/cofactor set that was originally responsible for photosynthesis.

"chemical imbalance" meant the protein imbalance/changes

I presume you mean homologous duplication. Use correct terms or you will be babbling.

So (from waaay above) you think unifying is the same as foundational? Or is that just a small part of it?

Evolution is foundational to biology not because one needs to refer to it when studying, say, replisomes or transcriptomics, although one can link the two, it is foundational because evoloution explains everything in biology, everything refers back to it, and everything can be linked, under it. It is the grand unifying theory of biology, in the same manner as atomic theory is the unifying theory of chemistry.

surely would throw up a LOT more ineffective/"dead end" organs than effective ones but we don't really see many of these... Do you know why that is?

You are incorrect. The reason for it is because of gene conservation. Deleterious mutations are eliminated by natural selection, and neutral mutations do not change frequency under selective pressure. A biological structure like an organ can only be generated in the context of selective pressure acting on certain genes, over a long lineage. Evolution is not a random process. The generation of biological structures requires the pressure of selection over a population to alter gene frequences. Indeed, when selection is relaxed, these structures will tend to fall into disarray over time, because anything which is not under selective pressure will rapidly accumulate deleterious mutations and be destroyed. Evolution does not "throw up" deleterious biological structures. Large scale biological structures can only be generated by selective pressure. Thus, you are shooting yourself in the foot, and are obviously very confused.

The principle of conservation is that which is behind the molecular clock. The clock is a controversial idea, and it doesn't run for every gene and hence for every characteristic. But we do know that the clock runs for highly conserved genes, and I shall tell you why. This is why we use highly conserved genes as the basis of genetical studies of phylogenetic trees. For some genes, the clock does not run at a constant rate because the conservation of their sequences can change depending on what is being naturally selected for. This is a big problem. But a highly conserved gene such as H2 or 16S will never have this problem because they are so central to biological life, and so finely tuned, that most mutations will destroy them and hence the organism that holds them, and as such, the clock runs very slowly and it runs very constantly. This is why they are used as a "master clock" to ascertain the change in base pairs between organisms, which, together with our inferred understanding of the relationship between taxa from the fossil record, will tell us how distantly related two organisms are on the basis of the number of base pair substitutions which have resulted.

The other sort of gene for which we will want to use in phylogeny is that which has no conservation whatsoever, which mutates solely on the basis of random frequency. The problem with this is that such genes will mutate out of existence very quickly. There were several proponents of the intelligent design movement who claimed that traits like the Kreb cycle set were put in place as "dormant" before they were needed, shaped by the creator of the mechanism in question. They were forced to retract that claim after they were cornerned by mainstream science and it was pointed out that a gene which serves no function will mutate out of existence very quick. Notice I say "gene", not "DNA sequence". The two are not the same so don't confuse them. A special sequence of unconserved but also undiscarded sequences called fibrinopeptides, which are discarded during fibrinolysis, form the basis of a "master clock" which, together with highly conserved genes, will tell us the relationship between organisms based on the rate of change of sequence. These sequences have no conservation, but they also serve a function. They are unique in that this function does not depend on their amino acid sequence, and as such, they are tremendously important for phylogenetics.

Your ignorance is astounding, but at least you admit to it... part of it.  Evolution can and has been observed.  It does not require a vast amount of time.  It is fallacious to believe that evolution requires a long time frame to be aparent.  Check out this thread, the appended article and then go and find the other articles that have existed where evolution is shown to have occurred, where it can be observed to occur and on rather small time scales.  Look to any virus or bacteria extant to see evolution virtually right before your eyes.  Just stop saying that evolution happens over a long time scale, too long of one to be observed; it just isn't true.

And the strength of the theory is not because there is no alternative explanation.  The strength of the theory is because it is capable of making 100% accurate predictions within its realm of explanation.  This is why gravity maintains as a theory.  It is not merely taken so seriously because there is no other theory that explains gravity, it is because the theory best explains gravity and makes perfect predictions based on the observable phenomena.  The Theory of Evolution is the compendium of evidence and laws that inform the foundation, and indeed constitute, the whole of biology as a science and is the main explanatory force behind the phenomena observed.  It has proved to be accurate when tested where other theories have failed the rigours of the scientific method.  This is how it is with all theories.  This is science.

If I have to repeat myself one more time, I will put a bullet through my head. There is no process difference between marked changes in lineages over long periods of time, and the short term changes that are more easily observed due to timescales. To say so is a continuum fallacy. The same processes that generate genetic innovations under which selection pressure can be generated, recombination, modular shuffling and the rearrangement of genetic circuits under homologous duplication and divergence. These processes are just as responsible for the creation of a new protein as they are for the existence of a beating heart. It is merely that in the latter process is the result of a greater number of mutations and the recombination of different preexisting structures, and hence is the result of a longer application of selective pressure. If you take two populations, and split them under the application of distinct and different selective pressures (thus generating a cladogenestic split), the longer you wait, the more marked genotype and phenotype divergence you will observe. This is the very principle upon which all phylogeny is based. To keep thinking in the fallacious and silly way you are, that is, by means of conjuring a nonexistent chasm between genetic changes and innovations and large scale biological structures, is once again a continuum fallacy. No matter how intricate and complex, everything in biology, from an eye to a flegalla to a finger to a brain, can be explained in terms of genes, genetic circuits, modular sequences of DNA. The innovations within these sequences based on random mutations which are then selected for or against based on fitness of the variation expressed in terms of phenotypes, will therefore determine the propogation of an allele and so a phenotyptic trait. This process can explain any phenotyptic trait based on genetics (hereditary traits).

Age is no excuse. I first read Douglas J Futuyma's Evolutionary Biology (the current edition being the standard textbook in university courses on evolutionary biology) when I was 17.

Yeah, but Biology is your interest... Mine is more engineering related but I like to look into other subjects too - and I warn you that biology (apart from languages and... now i think about it, possibly chemisty) is my weakest subject.

Although I think that age IS an excuse (as it is limiting), my point was more that it shouldn't be surprising that I don't know, as most people, <i>especially</i> at my age, don't.

Sorry I have been not very responsive these last few days - I haven't really had a break (nor will I for the next few days) but I'm not running off on you all - honest.

And please don't put a bullet through your head  - Who would I be able to ask stupid questions to then?

Ali

Careful with this one.  This is a speculation among some scientists, and there is substantial debate over whether or not intentional breeding manipulation can be considered real deviation.  After all, evolution gave us the intelligence to do it.  The exercise of our evolutionary survival advantage has increased the survival rate.  By every definition of evolution I've ever read, this fits.  Placing an arbitrary judgment of survival based on human value judgments is a philosophical error, since genes do not operate under our own philosophical paradigms.

 I was going to respond to this part of it but I'm a little confused. please clarify.

I understand and agree with the deviation part of your statement.

I also understand that because genes are pattern dependent  they have no philosophical processes.

Unless you thought that by using the word "stupid" I was making some kind of judgment, but that would be an assumption on your part. I do think the word "simple" would have been lest open to interpolation in that case.

Then try harder, you slacker!

Well, did anybody observe the evolution? Can we watch how live is coming from the ocean, evolving first into a fish, then into a reptile and finally into a human being. No, of course we can't see the evolution in front of our houses, we can't see it on TV or through a microscope or a telescope. All we can see are little changes. A butterfly is changing his colors over a few years. But nobody could see a fish evolving to a reptile or a monkey turning into a man. Do you know what that tells me? It tells me that atheists are believers too. They only believe something different than christians do. Sometimes they even believe into an scientological achievement or a proof for evolution that still has to come. But they believe it. Everybody is free to believe what he wants. But nobody should believe that his believe decides what is fact and what not.