Theories - Origin of Life

[AstraSequi]

So can we agree on what each of us means when we use the term mutations. As I have demonstrated there are differing views on what constitutes a mutation.
The talkorigins essay by Richard Harter states that :-

It is important to realize that mutations do not occur in response to the environment. They simply happen.

This appears to agree with berkley edu.
I have given you my understanding, could you let me know what your understanding is, so at least we don't get to talk across each other.

Again, I see no contradiction. I would add that some environmental factors can change the mutation rate (for example, exposure to UV light), but these are exceptions.

What I am describing (which you could call my "understanding," I suppose) is detailed above. Let me restate it as a specific example:
- Suppose a polar bear has a fur coat of a certain length, which is optimized to its conditions (too long and the bear will overheat, too short and it will freeze).
- Mutations are always happening, some of which will result in longer fur and some of which will result in shorter fur. However, these are suboptimal, so polar bears with these mutations don’t survive very well, and the mutations don’t get passed on.
- Now suppose the environment changes to become colder. The new optimum fur length is longer than the current length of the population.
- The next time a longer-fur mutation happens, that polar bear will survive. In fact, it will survive better than the polar bears without the mutation. Shorter-fur mutations continue to happen, but continue to be maladaptive – in fact, they now confer more of a disadvantage.
- As a result of the longer-fur advantage, the longer-fur mutants will leave more offspring.
- Since this applies to the polar bear’s descendents as well, the longer-fur mutants will eventually take over the population.


Also, if there was another population where it didn't get colder, then those polar bears would not change their fur length. The two populations would then have a difference between them, and sufficient differences would result in speciation. In fact, if polar bears were like certain birds and females were most interested in males that had the same fur length as themselves (this is called assortative mating), then this one change could be sufficient for speciation.

[AstraSequi]

There are random mutations that rearrange the DNA of the cell. These mutations are invariably the result of copying errors, breakdown in regulating functions like error correction, and DNA damage from environment like from chemical or UV radiation sources.

I agree, although I will point out that not all mutations rearrange the DNA - some of them just change it.

There are also more mutations in DNA, by orders of magnitude, as a result of regulated cell processes, than those that are random in nature.

Some mutations occur as byproducts of regulated cell processes, yes. For example, DNA synthesis is not perfect and introduces errors. That does not make the errors non-random – there is no way to predict where specifically the DNA polymerase enzyme will make a mistake.

A cell undergoing DNA synthesis is more likely to undergo a mutation than a cell that is not, but that is just a shift in the probabilities.

Barbara McClintock described various ways that an organism uses to respond to stress, among them by altering its own genome.

“Some sensing mechanism must be present in these instances to alert the cell to imminent danger, and to set in motion the orderly sequence of events that will mitigate this danger. The
responses of genomes to unanticipated challenges are not so precisely programmed. Nevertheless, these are sensed, and the genome responds in a discernible but initially unforeseen manner.

She ended her address this way

In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome. We know about the components of genomes that could be made available for such restructuring. We know nothing, however, about how the cell senses danger and instigates responses to it that often are truly remarkable.

(my emphasis)
http://www.nobelprize.org/nobel_prizes/ ... ecture.pdf

Yes, a cell under stress conditions might increase its mutation rate, including the rate of “restructuring” events such as inversions and translocations. This allows a greater diversity in the progeny, increasing the chance that some may survive. This does not imply that the mutations have become non-random.

I don’t know whether this has been shown definitively – this is not a peer-reviewed publication, after all (it is speculation, of which lectures often contain a lot – and is about 30 years old, far out of date). However, it makes logical sense – it might even be possible that some types of mutation are more likely to produce adaptations to certain kinds of stress, and these specific types of mutation are induced.

I will also point out that if you search for “restructuring” within the document, you will find her talking about it as something that occurs during species transitions.

For instance here then is an interesting review of some genomic changes(variations) found in nature. (1 December 2010) http://www.nature.com/nrg/journal/v11/n ... g2883.html
note what it says

Genomic rearrangements are associated with many human genomic disorders, including cancers. It was previously thought that most genomic rearrangements formed randomly but emerging data suggest that many are nonrandom, cell type-, cell stage- and locus-specific events. Recent studies have revealed novel cellular mechanisms and environmental cues that influence genomic rearrangements.

(again my emphasis)

Firstly, given that the paper is talking almost exclusively about genomic rearrangements that occur in cancer, I don’t think this helps you claim that these rearrangements are beneficial.

That being said – yes, mutations often do not form completely randomly, and can be highly influenced by the situational context. Sometimes, the influence is enough that you might call them “nonrandom,” at least with respect to certain parameters. This does not make them predetermined (that is, nonrandom with respect to every parameter), as you seem to be arguing. For example, meiotic crossing over is essentially a series of translocations, and they are nonrandom in that they only occur in a very specific circumstance, but the locations where it occurs cannot generally be predicted.

The changes are not random if you say that “random” means that every outcome is equally likely. If you think that is a potential confusion, it is probably better to call mutations probabilistic. There is another explanation of this at http://www.talkorigins.org/origins/post ... 11_01.html.

The reality is that most genetic changes occur as a result of cellular processes in response to stress, damage and copying errors and are rectified in various ways, (I have not taken account of the developmental changes that occur) while most other mutations which for some reason not corrected, are deleterious to the organism.

If you want to say this, you will also require evidence supporting the use of the word most in your first sentence.

You should also be aware that only germline genetic changes are relevant to natural selection. Changes that occur in somatic cells, which involve most types of environmental influences (including those that lead to almost all cancers) do not affect the next generation.

I haven't even begun to talk about transposons and their part in genome restructuring. All these processes are under the control and regulation of the cell as it responds to stress and the maintaining of its own equilibrium.

For the context of natural selection, transposons are just another way that genetic changes occur – and yes, in some cases they are not entirely random. For example, I think there is research showing that transposon activation in humans is more common in the germline. I'm not sure why you think they would be any different from other mutations with respect to the discussion though.

In the light of all this actual evidence (and with respect, not logic that you appear to rely upon) what does Natural Selection actually have to do?

Are you suggesting that cells intrinsically have a general capability to adapt genetically to environments without (random) mutation? It is quite easy to design experiments that falsify this.

For example - take a cell, form several clonal populations from it - so the populations are identical except for random changes. Expose them to stress, enough to slow their growth but not enough to kill them off. If they have a programmed response, they will all respond in the same way and at the same time. Your readouts will be the rate of growth (all of them should increase in growth rate at the same time, as they all adapt in the same way) and the DNA sequence (all of their genomes should have changed in the same way). This can be repeated with many different kinds of stress.

Or you could take some of those clonal populations and cause them to have a higher error rate in DNA synthesis. (Probably by addition of certain mutagens, or knockout/inhibition of a repair enzyme.) If the result is programmed and has nothing to do with the error rate, then the cell will again adapt to the stress in exactly the same way as the other cells (or possibly even worse). If the increased mutation rate is beneficial, as would be expected by natural selection, the higher-error cells will adapt faster.

Do you agree that these are reasonable and fair tests? If you're interested in science, you could probably think of even more ways to investigate. Of course, these or similar experiments were already done many decades ago, and were shown to be in favour of natural selection. You may, of course, repeat them for verification if you choose - the ability to do that is part of what makes science unique.

Where are the functional phenotypes that random mutation is supposed to have produced in order for NS to select from?

Answers have already been provided. For example, one such phenotype is the behaviour of hemoglobin containing the sickle-cell mutation.

It is no wonder that Darwin himself acknowledged he could recount no evidence for species change by NS.

I think you need to provide a quote – taken in context, of course. For example, the Galapagos finches are different species.

Also, if I recall correctly, most of the arguments and evidence involved showing that speciation through natural selection was plausible and not the only possible explanation. I am willing to be corrected though.

You should also remember that the evidence available to Darwin was far less than the evidence available today, and it is unsurprising that there were some things he could not explain. Even if Darwin did not have evidence for something (for example, the fossil record was extremely poor in his time), that does not mean the evidence does not exist today.

The reality is that NS has very eloquently described how species may survive but has nothing to say about how they arrived. Molecular biology was the great hope in answering the question of arrival, but it is only confirming what many have instinctively known, that this is not the answer.
Neo darwinism is stuck in the Neanderthal period of last century biology and (I am sorry to be blunt about this) no amount of huffing and puffing is going to alter that. (I am not suggesting that you are doing this, but others certainly are)

This is basically an assertion that speciation cannot occur, followed by a claim that evolutionary theory is out of date (relative to what?). I'm not sure what this adds to the discussion.

Of course, evolutionary theory has indeed advanced continuously, and the topics we are discussing have been known to biologists for some time. However, it is knowledge which has not been overturned to date. Some nuances have been determined (some of which you are clearly aware of), but the broader picture remains.

[AstraSequi]

Again, the possibilities are:
- the mutations might be common enough that they happen all the time
- the mutations might occur once or twice and then spread through the population by interbreeding
- the mutations might have already been present in the ancestral population

From my post above, I think it should be fairly clear that the third option is the most likely. However, even if it is incorrect, the others are still quite possible.

Sorry but the third possibility (the existing mutation) still has to deal with the actual issues of cell processes that researchers have identified and that I have already pointed to in my last post.

I told you why I didn’t want to suggest which one I thought was most likely – because you would immediately talk about only that one, and ignore the other two.

Again, all three possibilities are plausible, and there are probably more that I haven’t thought of. If you say that there is no plausible example, and three counterexamples are presented, addressing one counterexample is not sufficient.

Furthermore, I don’t know exactly what you’re referring to by saying “issues of cell processes,” so I don’t know how to address your response. (Presumably it is something I replied to above.)

I suppose most things are possible, it is possible that pigs will fly, but is that what we are discussing here, possibilities? I would argue not.

Well, you are arguing that certain things are not possible, right? Don't you think that the evidence presented by someone replying to such a claim (X is not possible) would involve showing that X is possible?

Speaking of which, I don't think you've clearly identified exactly what it is that you think is not possible – or at least, there are a number of things you think are not possible, but I can’t tell which is/are central to your argument, and a couple of them are also contradicted by some other things that you’ve said.

When I say central, that means the following – the things which, if you agreed were possible, would mean that you would also agree with the commonly accepted scientific view of evolution.

The interpretation "developed" is an inference that is not part of the data. Nobody has observed any population with no inversions.

Yes of course it's an inference, that is what data does. It helps us to draw conclusions. Do not most research papers have a conclusion section. Also I have not made any statement about populations without inversions.

You are the one who said that the inversions “developed.” Your quote: page 39, post 1.

Please note that three separate populations on three different continents developed these same inversions and in an “evolutionary” short space of time.

I can’t see any way to interpret this statement other than that they were not present, and then they were.

Also, the inferences are normally presented in the Discussion section. The conclusion restates the major inferences and speculates on what the importance might be if the inferences are true.

You are right variations can happen quite fast. However what is the data for “fins turning into legs” Please remember that this is also an “inference” but from what data is that inference drawn? Darwin couldn't find it in his pre molecular days, hence my question again, what has changed since then?

Firstly, there is nothing wrong with something being an "inference." If I let go of a paperclip a thousand times and it drops to the ground every time, I will make the inference that if I do it again, it will drop again. That doesn't mean it will drop, but there is no reasonable basis for claiming that it won't - unless you have access to further information (say, someone installed a powerful magnet in the ceiling since the last time you tried).

All predictions about how the world works are inferences. It is an inference that the next time you get in a car, you will arrive safely at your destination. This does not always hold, but it usually does, and so you make the inference that it will.

With regards to your question – there is not enough space here to give you a complete description of the evidence for macroevolutionary change (such as fins to legs). If you would like to understand that evidence, a complete treatment may be found at http://www.talkorigins.org/faqs/comdesc/, or a shorter one at http://en.wikipedia.org/wiki/Evidence_for_evolution.

[AstraSequi]

It depends what you mean by "unlikely." While any individual mutation is unlikely, that doesn't mean that it will not happen on a regular basis if you give it enough chances.

So the question therefore must be, how many chances does “enough” mean?

It depends on exactly how confident you want to be that you will get the desired result. For example, I might specify it to be the number of chances for which you will get that result on average about ten times. In this case, if the result had a one in a million chance, I would want ten million chances. Of course, I would probably get that result far sooner than the ten millionth chance.


Of course, for any particular mutation, it is possible to calculate the exact probability. (I realize that you have now started talking about multiple mutations as well ‒ I will address that below.)

Sample calculation:
There are several single point mutations in DNA gyrase which is sufficient to confer resistance to quinolone antibiotics. (Which, I will point out for your discussion with Luxorien, is clearly a beneficial mutation when you are being treated with these antibiotics.)

Let’s consider just one of these mutations, S83L in the gyrase A subunit, which is a C→T transition. (The first observation of this mutation was here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC245014/.)

E. coli has a mutation (without repair) about 1 in 300 replications.

Its genome size is about 4.6 Mb (4.6 million bases), so you have a 1 / 4,600,000 chance of the mutation hitting the base in question.

Since there are three possible bases it could change to, there is then a 1/3 chance of the mutation changing it to a T, rather than an A or a G.


A quick multiplication shows that the probability of this mutation happening is about 1 / 4,140,000,000. Each time an E. coli bacterium divides, there is a 1 / 4,140,000,000 chance of this mutation happening.

In other words, if I take 4.14 billion E. coli, about one of them will probably have the mutation. (In fact, approximately every possible E. coli mutation would be present around once.)

4.14 billion is fewer E. coli than you would find in a half-full test tube.

If I took that many E. coli and let them divide three times (multiplying the population by , you would produce the mutation de novo about 7 times. This would take about an hour.

The point is that generating any particular mutation is easy.

Suppose there is a mutation that has a one in a million chance of happening - you can call this unlikely. However, if a million fruit flies are born, then it will probably happen around once. If you then wait for a thousand generations, it will probably happen around a thousand times.

You are missing your own point here. The problem is that the second mutation has by necessity, have to build on the first for some fitness function to begin to arise. This is where your probability analysis falters. Your analogy refers to the same mutation arising. (the point you are making for your analogy)

So you understand that I wasn’t talking about mutations over time, but rather the likelihood of a single mutation, right? (Further answer in the next point.)

Also, I don’t know what you mean by a “fitness function.”

In order for an improved fitness/function to arise, the mutation must be different but also it has to add to the function of the previous mutation.

The probability for every mutation, by nature of its randomness, has to start from scratch every time.
So by your analogy of a thousand generations, the progressive mutation towards fitness/function will not occur around a thousand times. It will be orders of magnitude more.

Your statement implies that you are trying to use combinatorial probabilities where they are not applicable. You would only multiply if you were talking about multiple mutations that happened simultaneously.

The idea of progressive change is that the mutations do not have to happen simultaneously. Let us take the same example – mutations with a one in a million chance, which will still happen very frequently over a thousand generations of fruit flies. That is, they will happen individually around a thousand times each.

Even if one mutation is only adaptive if the first one has already been made (that is, the second one builds on the first, the probability is not low. The genetic context has changed by the time the second mutation happens. As soon as the first mutation happens and takes over the population, the second mutation cannot do anything but build on the first one.

The applicable probability calculation would be the chance that the first mutation happens at least once, followed by the second mutation happening at least once. (To be more realistic, you can also stipulate a several-generation time lag as the first mutation takes over.)

In fact, in this example (a thousand generations with each mutation happening about once per generation ‒ 40 years for a fruit fly), it would happen almost immediately. The first mutation would almost certainly occur at least once in the first couple of generations, you can give in a few more generations to become fixed, and then the second mutation will happen approximately once in every generation after that. In fact, you could get hundreds of sequentially adaptive mutations (if such a series actually existed) by the end of the thousand generations.

I will also point out that multiple mutations that happen simultaneously, even with the orders-of-magnitude-lower probabilities, are still very much within reach. This is especially the case in bacteria. However, the point is that it is not necessary to do this in order to build function on top of function.

Also please remember that mutations are invariably deleterious to the organism. Take for example the mutation that causes Cystic fibrosis. As I understand it, this is a mutation caused by the deletion of three nucleotides. This is a fairly common mutation and deleterious, it is in the nature of most random mutations.

You know that “invariably” means “always,” right? If that is the case, the third sentence of this quote (where you use the word “most”) is in contradiction with the first.

For NS to select for survival or “fitness” whatever that should mean, the mutation needs to be a positive one. Now since most of these mutations are deleterious, any positive one, has to not only evolve for greater fitness or function, but it also has to offset the downward pull of the many harmful mutations that are also taking place.

This is where you do use conjunctive probabilities – the harmful mutation has to happen in the same organism as the beneficial mutation. As a result, this occurrence is much rarer. If strongly harmful mutations were so common as to appear with high probability in every organism, then everything would be dying quickly whether they had beneficial mutations or not.

If they do happen to appear in the same organism, then yes, you have a conflict. Then, if the effect of the harmful mutation is greater, the double mutant will be selected out and the beneficial one will have to arise in the population again. If the effect of the beneficial mutant is greater, the double mutant would survive and take over the population, and eventually the harmful one would be reverted by another mutation. (Or, if the beneficial mutation is frequent enough, the double mutant would survive but would be outcompeted by an animal that had gotten only the beneficial mutant in the first place.)


Two other points:
- Actually, the majority of mutations are neutral – the majority of the rest are deleterious.
- To answer your comment in the first sentence: “fitness” always refers to the number of viable offspring left behind. However, it is often used to describe anything that correlates with the number of viable offspring left behind (for example, skill at avoiding predators) as well.

[AstraSequi]

Another thing to please keep in mind, these examples of random mutations provide evidence of what is termed micro evolution and in a negative way at that, the deterioration of the organism. Nobody as far as I am aware denies that these changes take place. The point is do these changes lead to new species formation.

(See the links I gave you above.)

And this of course leads to another related question. What evidence do we have of the positive effects of any random microevolutionary mutations?

You just said,

Nobody as far as I am aware denies that these changes take place.

If you are asking this question, it implies that you’re denying this anyways.

And again, examples have been given ‒ such as the DNA gyrase example I gave above, as well as in your discussion with Luxorien.

The body plan must be altered in some way for speciation to happen.

Definitely not. For example: changes in chromosome number, changes in behaviour (for example, mating rituals), enzymatic changes in the reproductive system, etc.

I would ask, what evidence that the segmented nature of the body plan of the fruit fly has changed throughout it's existence, regardless of how rapid its generation time may be.

Segmentation is perhaps the most successful body plan in existence. The three-segment body plan of the insects has not significantly changed since their common ancestor. It is entirely unsurprising under natural selection that some things do remain unchanged.

(And of course, the word successful refers to fitness)

Recall Richard Lenski's 22 year experiment with bacteria (I have covered this before). After over 50,000 generations in each of 12 populations (600,000 generations) no new species of bacteria arrived.

If you have covered this before, perhaps you have been informed that the term “species” does not apply in the same way to bacteria as to sexually reproducing organisms.

The appearance of the Cit+ strain (a change in one of the fundamental identifying criteria) is essentially as close as you can get to speciation for a bacterium. Lenski has made this point as well.

I don't know much about the Bonferroni correction...

Then look it up – this is how you learn.

The probability of something happening increases as the number of times it is possible to occur increases.

This is with regard to the same thing happening again and again. But for a new mutation to provide a positive outcome it must add to a previously positive one and in a positive way, to succeed. In other words (as I have previously stated) it must be a different type of mutation.

I have addressed this above – you want to use probabilities of successive occurrence rather than conjunctive occurrence.

Take the cystic fibrosis mutation (the 3 nucleotide deletion), it can repeat itself over many generations in a population, but it is the same mutation. It doesn't add anything.

Correct, because it is negative – it does not spread within the population. If it did, then everyone would have it, and every new mutation would have the potential to build on it.

Also in addition to this one that I have cited, I am informed that there are some 200 other mutations of this gene that have been documented. So mutation of this gene is fairly common. Only a few lead to the severe form of this disease while others cause lesser problems, but, there are no beneficial results.

Since people generally only get the CFTR gene tested if they are already suspected of having CF, it is unsurprising that only negative mutations are found.

I am not saying that there are positive mutations that occur in the CFTR, but only that doing tests specifically on sick people is unlikely to find any.

But by the way, did you know that CF mutations have been suggested to be protective against cholera? This is a similar idea as the sickle-cell mutation.

Systems biologists are increasingly recognising the robustness of cellular processes. Mutations (of all kinds) produce little phenotypic variation. If the mutation is serious enough the organism either becomes diseased or it dies.

This is just a restatement of the claim that all mutations are negative.

Your roll of dice analogy simply does not apply.

That is correct. The only point made by the analogy is that given enough chances, even the most improbable things happen – where “enough” depends on exactly how improbable the event is. If you want to look at changes over time that build on each other, you have to use a more complex analysis, as I detailed above.

Finally on what is the “scientific” view of mutations? Are they all random or are they also non random.

Science is a method for learning about the world. Definitions cannot be “scientific” or “nonscientific” except insofar as they were based on scientific information, so I’m not completely sure what you mean. (See the next point)

Mutations originate both randomly, and also as a result of cellular processes, non randomly.

This is about the process by which mutations are generated, and as such is not an answer to the question (which doesn’t really make sense, as I pointed out). It is also a restatement of something which I have already discussed.

If you want me to restate my earlier responses, it would be something like this: changes in DNA occur in a probabilistic way, and evidence suggests that some changes are more likely under different conditions. It is not generally possible to predict the exact mutation that will occur, nor the exact time of its occurrence. These changes in DNA are the genetic variation which can be acted on by natural selection to allow change to occur.

[AstraSequi]

Has this situation changed since Darwin's day? Can someone help with some evidence.

Most definitely. I suggest you read http://en.wikipedia.org/wiki/Speciation, and also any included citations if you want to investigate further. Please note in the opening paragraph, "Observed examples of each kind of speciation are provided throughout."

Thank you for the wiki reference, and I have studied it.
It does provide good descriptions of the different kinds of speciation evolutionary theory posits.

The page is not about “positing”, but observation.

It goes on to exemplify this:-

One example of natural speciation is the diversity of the three-spined stickleback, a marine fish that, after the last ice age, has undergone speciation into new freshwater colonies in isolated lakes and streams.

It provides a single reference in support of this, a 2000 paper.

I think you could select more than one example – one which does not have some measure of debate surrounding it, as this one seems to. You could find even more examples at http://www.talkorigins.org/faqs/faq-speciation.html, for example (which I probably should have linked last time). Or perhaps you might consider ring species.

The first point I noted in the wiki discussion was, this example appears to be about variation within a species. Nobody as far as I am aware disputes that variation within a species does occur.
...
So although they claim species divergence, they are still referred to three-spined sticklebacks (Gasterosteus aculeatus). I find that somewhat interesting.

And what do you infer from the knowledge that this is “somewhat interesting”?

It seems that they are different species, but nobody has yet gone through all of them (a difficult undertaking) to systematically record their similarities and differences and propose a new classification system. Or perhaps whether they are different species is not yet determined beyond doubt, and nobody will propose a new classification system until it is clear that one is necessary.

After reading more on this particular example, it seems that there are many different populations, some of which can interbreed with each other and some of which cannot (similar to ring species), and that it is therefore difficult to assign species identifiers to any group until it is decided on how to handle situations like this.

In a more recent study found in the Journal of Fish biology we have this paper
...
The introduction states that speciation is a continuum of 4 different stages, with the final one being the complete reproductive isolation, and this reproductive isolation is always associated with chromosomal rearrangements and environment independent genetic incompatibilities.

Yes, in sticklebacks, and they make this suggestion based on two previous examples. They say nothing about other organisms. You can also search for “rearrangements” within the document and note that the claim for requiring genetic incompatibilities tends to be placed with qualifying words like “may” and “seem.”

The paper then goes on to examine these 4 stages in connection with the stickleback.
1) continuous variation without reproductive isolation
2) discontinuous variation with minor reproductive isolation
3) strong, but reversible, reproductive isolation
4) strong and irreversible reproductive isolation

Only stage 4 can be classified as a speciation event and the paper points to only one example

Isn’t “only one example” sufficient to refute your claim that no speciation can occur? And as I have already shown you, there are sources which supply many more such examples.

Why have these sympatric pairs not proceeded to the point of irreversible reproductive isolation? One possibility is the limited time frame for their divergence, given that most freshwater populations were colonized from marine ancestors only after the last glaciations...This explanation is not entirely sufficient, however, given that genetic incompatibilities have not been documented across the range of G. aculeatus, including among populations separated for millions of years...

Another possibility, then, is that the divergent selection is not strong enough to generate irreversible barriers through ecological speciation. Equivalently, assortative mating may not be strong enough, perhaps because trait divergence is not sufficient for females to reliably or profitably discriminate against heterospecifics. Finally, irreversible isolation in sticklebacks may require specific genetic changes, such as chromosomal rearrangements.

It may be relevant to point out that they do not say no selection is strong enough to generate irreversible barriers.

Finally, achieving state 4 (strong and irreversible reproductive isolation) seems to require additional factors, such as chromosomal rearrangements, intrinsic genetic incompatibilities and extended periods of allopatry, all of which are less obviously linked to processes occurring along the rest of the speciation continuum.
Perhaps the greatest lesson that sticklebacks can reach is the value of plurality in the study of speciation. That is, speciation might often involve multiple and shifting geographic contexts and mechanistic drivers. This mosaic nature of speciation has also been suggested to characterize other taxa...and it might even be reasonably common in nature. The solution to Darwin’s ‘mystery of mysteries’ might therefore be considerably more complicated that proponents of parsimony might desire. Nature is not parsimonious.

Again, even if these “additional factors” are necessary, that does not mean that these factors can never be supplied.

The apparent necessity of Chromosomal rearrangements within the nucleus pose a significant problem, if speciation is the product of random mutations to the genome.

So your entire argument is that large-scale genetic changes are required for speciation, and that such changes are not possible?

First, the authors only suggest that there is such a necessity in sticklebacks, and you have taken it as fact for all species.

Secondly, you haven’t made any argument for why such changes actually aren’t possible.

We know the nucleus of each differentiated cell appears to possess an epigenetic mechanism.

Do you mean, “we know that the nucleus of each differentiated cell appears to be regulated epigenetically”? If so, then I agree (and the evidence for this is far stronger than “appears to be” – I would just use “is”).

There are lots of epigenetic mechanisms, not just “an” epigenetic mechanism ‒ histone acetylation, histone methylation, cytosine methylation, etc. Undifferentiated cells also have epigenetic mechanisms.

This mechanism regulates the position of each chromosome in the nucleus and thereby determines the way and timing of how expression takes place. We also know chromatin structure, the variation in histone 3D structure and so on are indeed regulated by this mechanism.

Agreed.

So the control of chromosome activity in the nucleus clearly cannot be the product of a mutation in the genome.

We are observing levels of information and control above and beyond genome information.

The proteins involved in epigenetic control (such as histones) are themselves encoded by the genome. They don’t appear out of nowhere.

Yes, there are some proteins which affect the expression of other proteins. This means that a mutation in a regulatory protein will also affect the expression of the proteins it controls.

All of these are not instigated or varied or regulated by mutations to the genome...

See the previous point.

...and yet this study (which is very detailed and is really worth studying in full) is concluding that chromosome rearrangement is a requirement for speciation, whereas neo darwinian evolutionary theory is fixated on random mutations of the genome.

Chromosome rearrangement is a mutation. Check the definitions that you gave earlier ‒ this is one of the ones you said you agreed with.

The term mutation can refer to any process that changes the genetic information in the genome, including DNA insertions, deletions and rearrangements.

And as already discussed ‒ rearrangements are random as well. Or to avoid giving the wrong impression, they are probabilistic.

Ones like Donald Forsdyke have long recognised this link between chromosomal arrangement and species specific traits, only to be castigated by the likes of Coyne and Orr with their gene centred views.

I think you need specific examples if you want to make such a general claim.

So I conclude that despite the wiki appraisal of speciation as being a darwinian process, the evidence suggests no such thing.

The discussion above only refers to the fact that speciation has been observed, not the mechanism ‒ observation and mechanism are, of course, two different things, which involve separate bodies of evidence.

Of course, since there are only two forces which are known to cause changes in species ‒ natural selection and genetic drift ‒ it is reasonable to conclude that one of these is the cause of speciation. The roles of each of these took some time to determine, but the evidence eventually showed that natural selection was probably the dominant factor.

I will also point out again that you are attempting to use one example only (and a complicated one as well), and trying to generalize to every species in existence. This is not a very strong line of reasoning.

[AstraSequi]

The question of “correct” mutations being random makes no sense when we are dealing with for example proof reading. This type of process requires some template to compare with in order to be “correct”.

No, I am not implying that there is some specification of “correctness” in evolution. I used the term “correct” as a shorthand to mean, “the mutation we are talking about, which will confer some selective advantage” – as opposed to any of the neutral or deleterious mutations that might occur instead.

How about checkpoint systems during cell division. Here again there must be some template by which the process is able to determine when the process is ready to move on to the next stage.

The checkpoint systems are the template. When certain criteria are fulfilled, the checkpoint proteins allow the system to move on to the next stage. If the criteria are not fulfilled, the checkpoint proteins prevent this.

And of course, mutations to the checkpoint systems will change the template, and the new template is then subject to natural selection. However, since this system is critical to cellular survival and many other systems depend upon it, it is already highly optimized and will not change very fast.

In other words there must be some body plan by which these mutations can be compared in order to make any determinations as to whether to continue or abort.

I don’t know what the reference to the “body plan” means. If you meant to say “template,” I have answered that in the previous point.

No one as far as I am aware has even adequately addressed the how cell differentiation can be the result of random mutations to the genome.

You made the same claim later, about the appearance of the genetic code. I will answer it there.

For example, if we put some bacteria in nutrient-rich media, they will always start to grow faster after some time. This experiment only takes about a week to run, and the change will always be in the same direction.

That is to say, we observe that natural selection produces the same result. This will happen for almost any bacteria we can grow - the new environment favors those bacteria that grow the fastest, so long as we allow enough time to pass.

The question is not whether the bacteria grow any faster, the question is does this produce any new species.

...That’s not what I was discussing.

The points I was making were that 1) the bacteria observably adapt to their environment and 2) the adaption is reproducible no matter how many times you run the experiment.

I was responding to your apparent view that if mutations are random, the same adaptation cannot arise independently more than once. Quote (page 39, post 1):

This is evidently a programmed response to climate (temperature) change... Please note that three separate populations on three different continents developed these same inversions and in an “evolutionary” short space of time.
How this can be the result of random mutations, which according to darwinian theory they would have to be, unless of course one is happy to play with unlikely statistics.

Of course, that does not mean that the adaptations are exactly the same ‒ the response is not programmed, as I discussed earlier. The mutations will occur at different times, and will often be slightly different. It is the phenotype which is the same, which is the important part.

The Lenski experiment has clearly shown that no new species has emerged despite all the mutations that occurred.

Replied above.

For a start there has not been enough time in earth's history for any probability theory to be used in connection with these ideas.

What is “not enough”? How much time would be enough? Also, which specific “ideas” are you talking about?

Even if you think that the world is less than 10,000 years old or something like that, there is plenty of time for at least some speciation to occur. I agree that you probably couldn’t make major evolutionary jumps, but you would still observe speciation happening.

I also point out that you said above,

You are right variations can happen quite fast.

Do you still agree with this statement, or do you have some meaning of “variations” that would not include the variation I am discussing in my probability example?

Natural Selection is not a force but simply the naturally selected result of random forces. The driving force in darwinian theory is the random mutations that allow nature to select from.

I think this is semantics. Both stages, the mutations and the selection, are required for species to adapt. If there are no mutations, no variation is generated and no change can occur. If there is no selection, only random change can occur.

This is not about semantics. Random Mutations are the driving force in Darwinian processes. The problem is that you have to rely on such vague terms as “enough chances” to try and justify the hypothesis.

My point was that I think “driving force” is a vague term, and I’m not sure how establishing it is important to the discussion. Again, both the mutations and the selection are required.

The enviromental stress in three different continents are not the same. What the researchers noted was that the climate/latitude was the common factor. That is why they made the link with global warming.

That is why I said:
In the most charitable interpretation I can think of, I suppose it is possible to make some assumptions and then say that their data is consistent with a completely deterministic model. However, you cannot say that it is evidence for such a model against natural selection, because natural selection can account for the same results quite well, and without the extra assumptions.

Well you are right. You can suppose it’s possible to make any manner of assumptions if you wish to be charitable. It may not refute NS but it is certainly evidence against as I stated

No, it is not evidence – that was the point. As a general principle, if two different theories make the same prediction, observation of the predicted result is not evidence for either theory.

If Theory A predicts that the sky is blue, and Theory B predicts that the sky is blue, and then we go out and look at the sky and it’s blue, that tells us nothing about which theory is correct. I apologize if I am being overly blunt.

If the capacity for change is limited as this researcher warns, then what happens to the theory? After all climate has always been on the change throughout life's history.

Natural selection does not say that the capacity for change is unlimited. It might perhaps be the case, but only given enough time - the rate of change over any particular time scale is limited by the amount of pre-existing variation in the population, and the rate of production of new variation (that is, the rate of mutation).

I haven't suggested that NS in unlimited, however it is attributed with going from Amoeba to Man. That's a very bold claim, so what is the evidence to back it up. [/quote]
...But that wasn’t what we were talking about. I was replying to the quoted statement, “If the capacity for change is limited.” It certainly looks like you were suggesting that natural selection only works if the capacity for change is unlimited.

Of course I can reply to this new statement as well, and I refer you to the pages I linked when we were discussing macroevolution above.

If the rate of change is too fast, the species is unable to adapt and goes extinct. Climate has never changed as fast as it is now in any point in Earth's history (save perhaps the mass extinctions, and of course they didn't go too well for life!)

It's not a question of whether the species goes extinct. Species do go extinct. The point is whether they change into new species. That is what Natural selection is supposed to accomplish.

I was trying to illustrate the concept that adaptation is always a race – the organism must adapt faster than the environment can change, and this is the criterion for when species go extinct. (In this context, “environment” broadly refers to any change that might affect the species’ reproduction.) I thought that this might help you better understand the paper.

Well actually I cannot think of any reason why Dr Huey would be disturbed, other than this change does not sit well with evolutionary theory.

Very well - it is related to what you said above. Drosophila is a highly successful species, with a very short generation time and the ability to adapt very quickly to new environments. When we see such a species changing very rapidly, it means that it needs to change that fast in order to stay adapted to the environment. (Or, in an even worse case, that its rate of change is at maximum, and it would be changing even faster if it could.)

This means that any less successful species, which cannot adapt as fast as Drosophila is adapting now (and which does not have other options such as migration), is likely to be in great difficulty.

In fact, I can tell you what the authors of the paper say, in their concluding paragraph:
The increasing numbers of examples documenting genetic (2–5, 8, 10, 11), as well as phenotypic (1, 2) responses, to recent climate change are not surprising from an evolutionary perspective, but nonetheless are disturbing from ecological or economic ones, because such changes signal inevitable disruptions in the distributions, population dynamics, and community interactions of organisms (1, 2).

(My emphasis.)

I am aware of their “not surprising from an evolutionary perspective” view but are they speaking from the perspective of speciation? The fact is they are not. The variations they are referring to are variation within species that appear to be governed by cellular responses to climate change. If natural selection was at work (in other words if NS was causing these changes) why would they be disturbing?
After all is it not expected that natural selection will result in changes such as these. They are disturbing because they don't sit very well with Natural Selection expectations.

To whom are they (supposedly) disturbing for this reason?

Previously, you were saying that the authors found it disturbing for this reason. I then gave you a direct quote from the authors saying that they found it disturbing for a different reason.

Also, did you understand my response? You didn’t comment on anything other than my last paragraph out of three.

I definitely agree with you that the authors know more about this topic than us. However, you will then need to accept these statements as well.

I accept their data not their “disturbing” perspective.

That’s fine, but
1) you previously asked me to accept something they had said because they had said it, which is the reason I made that comment. (Page 38, post 10).
2) we were talking about what disturbed him. I think that a direct quote answering that specific question is sufficient to provide a definitive answer.


(See below for my final post.)

[cyanodave]

I havent cared to read all 44 pages of reply's and I'm fairly certain you've enough material for your paper at this point though I feel certain things oughtn't be left out of your paper. With evidence provided by the Miller-Urey experiments it is known the general composition of our early atmosphere was capable of producing something that we today might identify as lifelike- presumably a protobiont with a primitive lipid membrane and some means of reproduction- presumably RNA. under proper circumstances these RNA molecules could multiply, though it is doubtful any kind of orderly cellular structure developed for millions of years, a simple strip of RNA may as well be classified as a living thing due to it's ability to reproduce.

[AstraSequi]

Also, observing rigorous data contradicting evolution would not be disturbing to scientists in the same way - it would be interesting.

So scientists are now relying on symantics are they?
...How then did the program arise?

I don’t understand what you mean.

I was pointing out that scientists are generally interested when it is shown that some previously accepted belief is false (and the scientists that do this usually become the most famous as well) – because it means that our beliefs have been made more accurate.

The common ancestor argument is an assumption. The creationists argue that the data this argument rests on is equally applicable to the creation argument..

I am glad to see that you understand the data is equally applicable to both arguments point which I referred to above.

Also, I don’t know what you mean by “the common ancestor argument.” If you are referring to the statement “a universal common ancestor existed,” then it is an inference from the data. One line of evidence supporting this is that the fossil record shows less and less diversity as you look in older and older rocks.

So this is no different to the “God did it argument” except in your case you are only moving the problem back

So in other words, you agree that a “God did it” argument (that is, a general statement with no evidence) is fallacious?

So you understand that “proving evolution false” would not mean that creationism were true, since the two are separate things. It is possible for both to be true (as long as you don’t insist on interpreting your scripture literally) or for neither to be true – although I see no need to publically endorse a position on that here since it’s not relevant to this argument.

The method by which the common ancestor arrived is no different to how Drosophila arrived.

Since this statement presupposes the existence of the common ancestor, I suppose that my inference about your “common ancestor argument” statement above is wrong? However, if so, I don’t know what you mean by “common ancestor argument.”

I also agree with the statement, with “the method” being natural selection. The common ancestor was not the first form of life, only the one from which all current life is descended.

Ernst Mayr one of the fathers of the Modern Synthesis in his Crafood Lecture put it this way.
http://www.biologie.uni-hamburg.de/b-on ... luence.htm

A most important principle of the new biological philosophy, undiscovered for almost a century after the publication of On the Origin of Species, is the dual nature of biological processes. These activities are governed both by the universal laws of physics and chemistry and by a genetic program, itself the result of natural selection, which has molded the genotype for millions of generations.

If you could describe why you quoted this (out of all the possible paragraphs in the speech), it would help me understand what point you are trying to get across. It doesn’t seem to be related to your following statements.

According to Mayr, God didn't do it. Natural Selection is what did it via common ancestry. That was his philosophy as he himself has put it. But you eventually get back to the single cell. He provides no explanation any more than Darwin himself did.

How did the cell emerge? There is no plausible answer that scientists can envisage other than by some outside agency.

There are most certainly answers that scientists find plausible. For example, http://en.wikipedia.org/wiki/RNA_world and http://en.wikipedia.org/wiki/Iron-sulfur_world_theory

These do not address the origin of the cell per se, but rather are theories about what came before the cell, which I’m sure you’ll agree is a prerequisite before the experiments to investigate how non-cellular life became cellular life.

And if we don’t know, is there something wrong with that? Science does not claim to know everything. However, there is no special reason to think that once we know enough, a problem which currently is unsolved will not be solved in the future. It has certainly happened enough times in the past, after all.

My argument is simple. The same process that caused the cell to emerge is the one that has caused the different species to emerge and that is by an outside agency.

This is not an argument, but rather an assertion. (Arguments have both premises and conclusions. )

If your argument is that we do not know how the cell emerged, therefore it was an outside agency, then that is argumentum ad ignorantium.

Craig Venter has shown that an outside agency (his team) have managed to demonstrate proof of concept. Albeit not in the creation of life but how an existing life form can be changed by design.

This is affirming the consequent. “It is possible for an outside agency to manipulate life; life came into being; therefore an outside agency was the cause.”

However in his intellectual arrogance Ernst Mayr classically contradicted his own argument. His philosophy as he states it, is “governed both by the universal laws of physics and chemistry by a genetic program” (his words).

I don’t see where the contradiction is. All I interpret from these quotes is a number of statements about natural selection ‒ and I also infer Mayr felt that natural selection (the unifying principle of biology) was an important consideration in the philosophy of biology, which I imagine is probably unremarkable among these philosophers.

Also, I am sure you know that science does not hold the words of any individual scientist as more important than the next. Newton was wrong about many things, Darwin was wrong about many things, and no scientist has any trouble saying so. Authority (at least ideally) derives only from the experiments that you are capable of and the results you derive from them.

I think this might be something you’re having trouble understanding. A quote from a famous scientist does not mean that they were right – in fact, it doesn’t even say anything about the current state of knowledge unless it was made in the last few years. Even scientific papers have some chance of being wrong or containing wrong statements. I’m not saying that Mayr was necessarily wrong about any particular statement, but you seem to be assuming that I (or “scientists”) must agree with him simply because he said it.

(I can’t think of any other line of thought that makes these quotes relevant to the discussion.)

Every scientist knows that a program be it genetic or otherwise does two things.
1) It uses natural forces which are governed by universal laws
2) It injects decision nodes into the process to over ride that natural progress and directs (governs) towards a specified goal.

I’m not sure about “every scientist” – are you including those which don’t even work with programs?

Anyways ‒ is this meant to be a definition, or a description? If a definition, where does it come from? If a description, what is the definition and how do these characteristics derive from it?

If it is meant to be a definition, why not simply “A sequence of instructions that perform a specified task”? (slightly modified from the Wikipedia definition of “Computer program.”)

He then goes on to state as if it were a fact that it was natural selection that created this program.

I imagine that he was speaking to an audience of scientists, and thus felt no need to justify something that everyone in his audience already knew the evidence for.

What decision node has natural selection injected into a process governed by the universal laws that has resulted in this genetic program?

I imagine that you could analyse the Tree of Life using decision theory, but the Tree of Life is not itself a decision tree.

The term “decision node” implies a single point of decision. Species do not reach a certain point in time and then get “forced” to choose one or the other path – change happens gradually, every generation, including when speciation is not occurring.

Natural Selection has to work on what is already there, that is why is regarded as a selective process. It does not create anything let alone inject decision nodes into any process.

Natural selection works with what is already there, plus what is generated by mutations.

If you wanted to use an actual decision tree, it would involve every occurrence (action or random event) ever done by or to every single member of the species that was relevant to its reproduction or lack thereof. On this level, natural selection most certainly is acting at the decision nodes – at every node, there is a change in the likelihood that the organism will reproduce.

For example how is the genetic code(s) the result of natural selection. There is no answer yet according to Mayr and all those who follow his philosophy, natural selection has somehow done just that. It is a dogma nothing else.

Not really. The inference is something like this: the Theory of Evolution has accounted for the vast majority of the evidence, no other explanation can do this to nearly the same degree, therefore it is reasonable to conclude that it probably can account for the rest of the data as well.

It is the same kind of inference as “the sun has always risen in the past, therefore I think it highly likely that it will do so tomorrow as well.”

You may dispute the premises, but if you do not (and Mayr himself probably did not), then the inference itself is quite reasonable.


To be specific: no, I do not know how natural selection built the genetic code. For all I know, it didn’t ‒ for example, perhaps it was built by an external agent (say, aliens with advanced technology). However, I see no reason why natural selection couldn’t have been responsible, so without external evidence I see no reason why I should go against Occam’s Razor and postulate an additional factor in my model.

Actually - what do you mean when you say "programmed"? A definition might help to clear up any misunderstanding.

Yes I did use the term programmed. I am not alone am I?

I already answered this before ‒ this is not an answer to the question.

If the change is dramatic (as you are suggesting) then new species would be expected to arise.

Speciation requires a) differential selection on different parts of the population, b) very low gene flow between those two parts of the population, and c) the low gene flow to be maintained until enough change has occurred to prevent any future interbreeding. (There are other types of speciation, but they are not as well understood.) The authors point out in the paper that criterion b is not met - in fact, that the gene flow is unusually high. As a result, criterion c cannot be met either.

Why would that be disturbing? Surely this is the natural way, according to the theory

As mentioned above - the authors say it quite well. Of course, it is not as disturbing for the future of life on earth as a whole, which will probably carry on no matter what we do.

Your assumption is that climate change is man made. You appreciate that the debate around this is quite vigorous.

This is very much a non sequitur. I was talking about the results of climate change ‒ and pointing out why it would be disturbing, which is what you asked me to answer. Of course, man-made climate change is quite uncontroversial among scientists, but that is not the issue I was responding to.

Also, you fused two of my replies to each other and only responded to the second.

Logic does not necessarily reflect reality as I have pointed out to you before. It can only be used if it is based on evidence, and with respect that is where your problem is

So you are saying that logic only reflects reality if the premises of the argument are true? I agree with that.

I also agree that if the premises of an argument are true (and the logical argument itself is correct), then the conclusions are also true.

I also agree that for an inductive argument, if the premises of the argument are true (and the logical argument itself is correct), and the inductive argument has been shown to be correct many times in the past, then there is no reason to think that the conclusions are not true. This does not mean that the conclusions are true, but that it is unreasonable not to proceed under the assumption as if they are, until more evidence can be gathered.

...this is the price one has to pay for dealing with what is essentially a philosophical position trying to pose as science.

But you agree that if something is supported by evidence, then it falls under science? Just to make sure that we share common ground on this.



Thank you for the discussion.

[wbla3335]

Thank you for the discussion.

Wow. You have far more tolerance of deniers than I do. They can resemble bricks sometimes, so I hope your efforts haven't been wasted. Good job, though.

[einfopedia]

there are 7 theories of a life.
Panspermia

Perhaps life did not begin on Earth at all, but was brought here from elsewhere in space, a notion known as panspermia. For instance, rocks regularly get blasted off Mars by cosmic impacts, and a number of Martian meteorites have been found on Earth that some researchers have controversially suggested brought microbes over here, potentially making us all Martians originally. Other scientists have even suggested that life might have hitchhiked on comets from other star systems. However, even if this concept were true, the question of how life began on Earth would then only change to how life began elsewhere in space.

Simple Beginnings
Instead of developing from complex molecules such as RNA, life might have begun with smaller molecules interacting with each other in cycles of reactions. These might have been contained in simple capsules akin to cell membranes, and over time more complex molecules that performed these reactions better than the smaller ones could have evolved, scenarios dubbed "metabolism-first" models, as opposed to the "gene-first" model of the "RNA world" hypothesis.

RNA World

Nowadays DNA needs proteins in order to form, and proteins require DNA to form, so how could these have formed without each other? The answer may be RNA, which can store information like DNA, serve as an enzyme like proteins, and help create both DNA and proteins. Later DNA and proteins succeeded this "RNA world," because they are more efficient. RNA still exists and performs several functions in organisms, including acting as an on-off switch for some genes. The question still remains how RNA got here in the first place. And while some scientists think the molecule could have spontaneously arisen on Earth, others say that was very unlikely to have happened.

Other nucleic acids other than RNA have been suggested as well, such as the more esoteric PNA or TNA.

Chilly Start
Ice might have covered the oceans 3 billion years ago, as the sun was about a third less luminous than it is now. This layer of ice, possibly hundreds of feet thick, might have protected fragile organic compounds in the water below from ultraviolet light and destruction from cosmic impacts. The cold might have also helped these molecules to survive longer, allowing key reactions to happen.


Deep-Sea Vents

The deep-sea vent theory suggests that life may have begun at submarine hydrothermal vents, spewing key hydrogen-rich molecules. Their rocky nooks could then have concentrated these molecules together and provided mineral catalysts for critical reactions. Even now, these vents, rich in chemical and thermal energy, sustain vibrant ecosystems.

Community Clay

The first molecules of life might have met on clay, according to an idea elaborated by organic chemist Alexander Graham Cairns-Smith at the University of Glasgow in Scotland. These surfaces might not only have concentrated these organic compounds together, but also helped organize them into patterns much like our genes do now.

The main role of DNA is to store information on how other molecules should be arranged. Genetic sequences in DNA are essentially instructions on how amino acids should be arranged in proteins. Cairns-Smith suggests that mineral crystals in clay could have arranged organic molecules into organized patterns. After a while, organic molecules took over this job and organized themselves.


Electric Spark

Electric sparks can generate amino acids and sugars from an atmosphere loaded with water, methane, ammonia and hydrogen, as was shown in the famous Miller-Urey experiment reported in 1953, suggesting that lightning might have helped create the key building blocks of life on Earth in its early days. Over millions of years, larger and more complex molecules could form. Although research since then has revealed the early atmosphere of Earth was actually hydrogen-poor, scientists have suggested that volcanic clouds in the early atmosphere might have held methane, ammonia and hydrogen and been filled with lightning as well.

[scottie]

Sorry for being out of the loop for a while.
My early childhood bout of chicken pox has revisited me in the form of shingles and has left me low for about ten days. Still not over it but have got back online to have a look at progress, if one could refer to any of wbla3335 posts as scientifically progressive
AstraSequi
Thank you for the time you have put into your final response. I will read through it all, that amount of effort is certainly worth due consideration.

Luxorien
Thank you also for your response. I will read and digest. I did prepare a little information to post on antibacterial resistance before I went down, so I will put it up later for you to comment on if you wish.