One-on-One:Questions about Evolution, MrJack and Truppenzwei

[Truppenzwei]

Hi,

Basically in this thread I'm wanting to ask a few questions in regard to evolution as much so that I can try and pin down exactly what evolution is and isn't, and what the science behind it is.

MrJack has kindly agreed to allow me to pick his brains on this subject.

So my first question to MrJack is:

What exactly is Evolution?

Lets begin there

 

[Truppenzwei]

Oh. and feel free to point me at an appropriate website/reference if you think it would save you having to regurgitate what that site is saying.

For instance Ive been going through the stuff here would you say that it pretty well sums up evolution.

If so then I'm perfectly happy to use that site as a reference for the various terms and the like and concentrate on my more in-depth questions.

 

[Mr Jack]

Hi Truppenzwei,

I hope I'll be able to answer your questions to your satisfaction and we can have an enjoyable and useful discussion.

Oh. and feel free to point me at an appropriate website/reference if you think it would save you having to regurgitate what that site is saying.

I generally prefer to debate in my own words rather than point to websites. Otherwise I find we end up arguing over what somewhat else thinks.

For instance Ive been going through the stuff here would you say that it pretty well sums up evolution.

I've looked through a bit of it, and it looks pretty good although I'd take issue with a couple of it's statements (more on that later). I'm happy to use it as a reference.

I shall try to have an answer to your first question ready to post later today.

Cheers,

Mr. Jack.

 

[Mr Jack]

What exactly is Evolution?

In this discussion, I shall assume we're talking about Biological Evolution or The Theory of Evolution rather than any of the other meanings of the word 'evolution'. I've also chosen to leave out the evidence from this answer, we can discuss that later as you see fit.

Evolution is the scientific theory developed from Darwin's work Origin of Species - the central theme of which is decent with modification by natural selection. It's a big subject so I'll break it into pieces.

The first part is Descent with Modification. This simply says that a creatures children are similar but not identical to their parents. In Darwin's time, no mechanism was understood for this process. Modern genetics allows us to understand how it works, and we can now track the transfer and alteration of genes. Genetic copying is not perfect, so each generation contains a small number of errors (which we call mutations).

The central part of the theory is the mechanism proposed by Darwin: Natural Selection. Natural Selection is really very straight forward, it says that individuals that are more successful will come to dominate the population. In practical terms the success of an organism can be measured by the number of grand-children it has (grand-children rather than children because having lots of children who die young or never breed is no use). It should be obvious that organisms that are having more grand-children will end up forming a larger portion of the population than those who are having fewer. Note that this success (known as fitness) may not correspond to what we would subjectively identify - for example, the fittest bear may not be the biggest and strongest because their energy needs are higher and they could suffer in times of drought.

This is, of course, complicated by sexual reproduction. In each generation, most organisms do not produce exact copies of themselves but mix their genes in with another's. So what, in fact, we should be looking at is the effect of genes (and the traits they cause) on the success of an organism and what Natural Selection is doing is increasing the proportion of the population that carry the given gene - this is what Dawkins is talking about when he uses the term 'Selfish Gene'.

When we combine Descent with Modification and Natural Selection we get Evolution. The theory is that over time mutation (and genetic recombination) will produce new solutions to problems (faster running, better wings, better eyesight, etc.) and that Natural Selection will constantly keep picking the one that works best. Now this level of Evolution is not particularly interesting, so far we've got dogs that run slightly faster than their forebears and moths that are a darker shade in industrial cities. The big claim made for evolution is that this mechanism is sufficient to explain the apparent design we see in all life today, including such marvellous examples as an eye, a bird's wing or an ant's social structure. An important point to remember is that evolution is not directed, there is no end goal. At any time it is simply picking what works best. This strictly limits the solutions that evolution is capable of finding since each one must be a step-wise improvement (or at least neutral with respect to fitness).

And this is were we come to the third portion of Evolution: Common Ancestry. Common Ancestry is the claim that similar organisms today evolved from common ancestors in the past (this is a slightly different claim from the Single Common Ancestor claim I will discuss below), so Coyotes and Wolves evolved from a now extinct Canid, Zebras and Horses from an extinct Equid and humans and chimps from an extinct ape. The evidence for Common Ancestry comes from two main sources: the fossil record and genetic analysis.

Most evolutionists believe that all life on earth evolved from a Single Common Ancestor, all believe that all animals evolved from a single common ancestors. According to Evolution we can construct trees of ancestry going back into the past, the further we go back the more the species alive today will converge in their ancestry. For instance, all mammals and reptiles converge to a single ancestor around 500 million years ago - the first vertebrate. The direct evidence for Single Common Ancestry lies in the use of DNA throughout all living creatures (viruses, incidentally, are not commonly thought of as alive - although I think they should be - scientists differ on whether viruses and all other life share a common ancestor), the indirect evidence comes from the simple convergence of evolutionary trees which, if extrapolated, leads inevitably to a single point of convergence. If Single Common Ancestry turned out to be false that would not scupper evolution as a whole. This is not true for either of the three points above.

The final areas of Evolution are Historical Evolution and Non-adaptive selection. Historical Evolution is the attempt to reconstruct as exactly as possible the actual evolutionary pathways that led from one species to another, and establish the relationships between existing species. Non-adaptive selection deals with genetic change in populations which is not linked to an individuals adaptedness: this includes things such as genetic drift as well as events such as lightning strikes and volcanic explosions.

You'll note that certain subjects commonly associated with evolution don't appear above. Abiogenesis (the origin of life) is not part of evolution, although any naturalistic theory of life must seek to explain it; Abiogenesis is not part of evolution because it cannot be explained through Descent with Modification as there is no descent before life. Stellar Evolution (the Big Bang, the formation of galaxies, the solar system, etc.) is also an separate subject, much more to do with physics than biology, as is Geology, specifically plate tectonics, river formation and the like. These subjects are not separated to avoid criticism of evolution but because they cannot be explained using the mechanism of Descent with Modification followed by Natural Selection that forms the centrepiece of evolutionary theory.

Does this answer your question?

Mr Jack.

 

[Truppenzwei]

What exactly is Evolution?

In this discussion, I shall assume we're talking about Biological Evolution or The Theory of Evolution rather than any of the other meanings of the word 'evolution'. I've also chosen to leave out the evidence from this answer, we can discuss that later as you see fit.

Agreed.

I've not bothered quoting the rest of you stuff as I think it pretty much gels with what I read at the berkeley site and I am willing to take what you have stated as our "working copy" so to speak of what evolution is.

Now within evolution there is micro and macro evolution where in essence micro evolution is change within a species while macro is change that transcends the species boundary, i.e. causes speciation

As far as I can make out they both use the same mechanisms it is just that macro evolution apparently takes much longer.

In essence microevolution+time=macroevolution, would you agree?

I'll proceed for now on the assumption of agreement and will backtrack later if necessary.

When I look at the mechanisms that evolution uses I think that on one level they do seem reasonable, and as far as I can make out they are relatively well proven. I think that with a few caveats microevolution could be seen to be a fact.

Now please not that by this I am not buying all the baggage of microevolution, for instance the example you made a minor reference to of moths getting darker due to industrial pollution is actually something that has not been scientifically proven, if anything it has been scientifically disproved.

However that aside I think there is definitely enough scientific evidence to say that genes definitely change over time and in essence that is what evolution is about.

However what I do have issue with is the whole idea of macroevolution.
There seems to be absolutely no valid scientific basis for this at all - it instead seems to be a spurious leap.

The whole concept to me of a common ancestor for all life seems a bit of a leap considering the evidence.

In fact a lot of the "evidence" for common ancestry can be put down to how an organism is classified. It would be very easy to apply different characteristics and make a very different evolutionary tree which would be just as scientifically valid and give very different results.

Also the fossil record to my mind seems to be given an awful lot more weight than it deserves. - take the coelocanth according to the fossil record it died out yonks back - yet it is still here - so what does that mean for the whole concept of stratification?

As for the whole dating of the fossil record - that seems a very dubious exercise from a scientific point of view as well.

Now I don't want to come across like I'm getting at you Mr Jack - I'm just wanting to try and get to the bottom of what evolution is and what the evidence for it is. I'd appreciate if you could come up with some answers to my queries above. Just to quickly restate I think that I could generally say that I accept microevolution (in general, again like yourself there are a few points where I differ from the consensus opinion i.e. I think you are right about viruses)

I hope this post isn't too rambling Mr Jack - or can I call you Jack? Let me know if you need me to clarify anything.

 

[Mr Jack]

Hi Truppenzwei,

There's quite a few questions in your post, each of which could do with a long answer. It would be helpful to me if we could try and concentrate on one issue at a time.

Now within evolution there is micro and macro evolution where in essence micro evolution is change within a species while macro is change that transcends the species boundary, i.e. causes speciation

I dislike the terms micro- and macro- evolution, apart from anything else they are very rarely used in scientific literature and differently defined by different people. However, if we proceed with the definition you give above and disregard the difficulties in precisely defining what a species is, I should point out that macroevolution has been observed both in the laboratory and in the wild (ref)

As far as I can make out they both use the same mechanisms it is just that macro evolution apparently takes much longer.

In essence microevolution+time=macroevolution, would you agree?

This is where I take issue with the terms micro and macro, because they are defined by their outcome, not their process it's very hard to say that. Some species can undergo large amounts of genetic change and remain a single species, others can change to a new species in a single step - most notably through polyploidy (chromosome multiplication) in plants.

Now please not that by this I am not buying all the baggage of microevolution, for instance the example you made a minor reference to of moths getting darker due to industrial pollution is actually something that has not been scientifically proven, if anything it has been scientifically disproved.

Have you been reading Well's Icons of Evolution per chance? The change in moths is most certainly scientifically proven, although no tests were done which would establish that the cause of that change was natural selection the data fits exactly with that model. Well's spends a lot of time (as I understand it, I have not actually read the book) arguing about the photos used being staged. This is true, some of the photos were staged. However, this has no bearing what-so-ever on the evidence presented in the research which was based on incidents of melanism in moths caught in traps, and an analysis comparing this to the level of pollution. See here for more details

In fact a lot of the "evidence" for common ancestry can be put down to how an organism is classified. It would be very easy to apply different characteristics and make a very different evolutionary tree which would be just as scientifically valid and give very different results.

This is simply not true. On several counts: firstly, the classification systems used are not arbitrary and not based on a single feature. While morphology does not define a single clear tree of life it does not allow you to create "very different" trees (certainly not for "higher" life forms such as mammals, reptiles and birds - it's much less clear cut for things such as bacteria) - there are too many features that define the tree and need to matched according to similarity so you couldn't match up coyotes and ocelots or even spider monkeys (a new world monkey) and vervet monkeys (an old world monkey) and still have a coherant morphological classification system. You should also realise that the classification system we still use today is very similar to ones developed before evolution was even proposed, yet alone accepted - more on this later.

Secondly, there is strong agreement between trees developed based on morphology (comparing the physical structure of living animals), genetics (derived used genetic analysis of living animals) and stratiography (derived from physical comparisons of dated fossils). Not only are these three lines of evidence independent, but one of them was developed before evolution was even thought of. What's more, the agreement between genetic and stratiographic trees increases with the number of fossils we have to work from! This, to me, is extremely strong evidence for evolution. If evolution is not true, why should these three totally independent sources of information give the same result?

Also the fossil record to my mind seems to be given an awful lot more weight than it deserves. - take the coelocanth according to the fossil record it died out yonks back - yet it is still here - so what does that mean for the whole concept of stratification?

Coelocanth is not a species, but a type of fish - the Coelocanths alive today are not the same as the ones found in the distant fossil record. It's a type of fish that used to be very common and is now found only in a few deep sea locations (incidentally, if you are interested in Coelocanths A Fish out of Time is a very readable book on the subject). The fossil record is inherently patchy because most creatures that die never become fossils, instead they rot away and disappear from history without trace, what's more we have only access to a very patchy portion of what is down there. Most fossils haven't been found. That a relatively rare, deep sea fish can fail to appear in the fossil record is no great surprise.

It's also no great surprise that a type of creature can survive that long without undergoing any great change. Evolution is driven by changes in the environment (which includes the effect of other creatures), once a creature has found a niche to which it is well adapted it can usually remain in that niche for a long time.

As for the whole dating of the fossil record - that seems a very dubious exercise from a scientific point of view as well.

That's too vague a comment for me to respond to, I'm afraid. Please elaborate?

Regards,

Mr. Jack.

 

[Truppenzwei]

Hi Truppenzwei,

There's quite a few questions in your post, each of which could do with a long answer. It would be helpful to me if we could try and concentrate on one issue at a time.


I dislike the terms micro- and macro- evolution, apart from anything else they are very rarely used in scientific literature and differently defined by different people. However, if we proceed with the definition you give above and disregard the difficulties in precisely defining what a species is, I should point out that macroevolution has been observed both in the laboratory and in the wild (ref)
Regards,

Mr. Jack.

I think concentrating on one thing at a time is a good idea and so will concentrate on the first thing in your post cause that seems the most sensible way of doing it.

Now if I look at your reference it reinforces my point that whether or not speciation (ie macro-evolution) has occurred all comes down to one basic question - what makes something a different species.

For instance - one could look at birds as being a species and leave it at that. Or you could say well all the green ones are one species and the yellow ones are another species or the ones with big beaks are one species and the small beaks are another - but it is all just an abstraction.

 

[Mr Jack]

Hi Truppenzwei,

Now if I look at your reference it reinforces my point that whether or not speciation (i.e. macro-evolution) has occurred all comes down to one basic question - what makes something a different species.

I've found a better reference here. It deals with several of the species concepts in some depth and also gives more details on observed speciation.

The concept of a species considerably predates the concept of evolution, initially it was based on morphology, and believed to be a classification of eternal and unchanging groupings (kinds, if you will). Later extensions brought ontogeny and behaviour into the system of classification to help distinguish species, and the latest in this line of species definition is to apply genetic analysis. However, this approach is very ad hoc and doesn't really constitute a formal definition.

The most commonly cited species definition is that two groups of animals are different species if they cannot reproduce. The trouble with this definition is that it is extremely difficult to test and is totally inapplicable to asexual organisms and extinct organisms and also has problems with hybridisation - for example, mules come from a donkey and a horse, but we don't wish donkeys and horses to be one species. Hybridisation is more of a problem with plants were fertile hybrids are much more common. Some have therefor refined the definition to 'don't reproduce' rather than 'can't reproduce'.

This leads us to the Biological Species Concept (BSC) which defines a species as a 'reproductive community' - in other words the set of individuals who could potentially pass genetic material between themselves. This serves well enough, but is still very difficult to test in the wild and difficult to apply to asexual species (particularly as horizontal gene transfer in bacteria can occur between different species).

You can read about the other attempts at defining species at the link above. I'll not trot over any more of them here, but instead discuss why a species is hard to define from an evolutionary point of view, and why it really isn't that relevant to evolutionary theory anyway.

If evolution is correct, then the concept of a species has no physical reality. A species can never be precisely and formally defined because the boundaries are always in the process of changing, instead of there being neat dividing lines between species we should see a continuum of change. From things we could unambiguously describe as different species (e.g. a blue whale and a house cat) to cases where it's unclear (e.g. ring species or easily hybridising forms of plants and butterflies).

Secondly, the vagueness of the species concept doesn't matter to evolution because it deals with individuals and populations not species. A population can be a species, or simply a small part of a species isolated by some means (a mountain, an ocean, vagaries of mate selection, etc.) - it doesn't even have to be entirely isolated to start with. You can formally define evolution without ever mentioning the term species.

Does that answer your question satisfactorily?

Cheers,

Mr. Jack

 

[Truppenzwei]

Hi Truppenzwei,

If evolution is correct, then the concept of a species has no physical reality. A species can never be precisely and formally defined because the boundaries are always in the process of changing, instead of there being neat dividing lines between species we should see a continuum of change. From things we could unambiguously describe as different species (e.g. a blue whale and a house cat) to cases where it's unclear (e.g. ring species or easily hybridising forms of plants and butterflies).

Secondly, the vagueness of the species concept doesn't matter to evolution because it deals with individuals and populations not species. A population can be a species, or simply a small part of a species isolated by some means (a mountain, an ocean, vagaries of mate selection, etc.) - it doesn't even have to be entirely isolated to start with. You can formally define evolution without ever mentioning the term species.

Does that answer your question satisfactorily?

Cheers,

Mr. Jack

I agree with a lot of what you are saying about species definition and I accept that defining things as species predates the theory of evolution.

Also I could quite happily classify a blue whale and a house cat as the same species - animal - It is all about where you draw the lines separating "species" from each other.

I would have to sort of disagree with you where you say the vagueness of the species concept is irrelevant to evolution. I would agree that if we confine evolution to mean the genetic change in a population over time then the species definition issue is irrelevant. In essence I'm quite happy to accept that the genetic makeup of a population changes over time - indeed I would happily say that this is proved by science.

However it is when the whole concept of common ancestry comes into play that I get a bit dubious about the whole thing. Now we agreed earlier on that abiogenesis isn't part of evolution, that evolution starts where there is a reproducing population ( I think that was the phrase) Now this is commonly taken to mean where the single common ancestor started reproducing - however why can't we have multiple ancestors at the same point in time and evolution (i.e. changing genetic makeup) has progressed from that point in time on each of those "species" - wouldn't that give us the same results as we see today? Isn't it as valid a hypotheses? Please note I'm not saying anything about where this bunch of ancestors came from because that isn't part of evolution.

Is this an invalid idea?

 

[Mr Jack]

Hi Truppenzwei,

Also I could quite happily classify a blue whale and a house cat as the same species - animal - It is all about where you draw the lines separating "species" from each other.

Only if you are going to ignore the history and meaning of the term 'species' and used it to simply mean group. We may not be able to give a precise formal definition for the term but we can use it informally in most cases without ambiguity. Incidentally there is a group that already contains house cats and blue whales - placental mammals.

However it is when the whole concept of common ancestry comes into play that I get a bit dubious about the whole thing. Now we agreed earlier on that abiogenesis isn't part of evolution, that evolution starts where there is a reproducing population ( I think that was the phrase) Now this is commonly taken to mean where the single common ancestor started reproducing - however why can't we have multiple ancestors at the same point in time and evolution (i.e. changing genetic makeup) has progressed from that point in time on each of those "species" - wouldn't that give us the same results as we see today? Isn't it as valid a hypotheses?

We could indeed have multiple ancestors that evolved separately according to the mechanisms of evolution. However, such a scenario would be extremely unlikely to produce the situation we have today (depending somewhat on what you suppose those ancestors to be). There are several lines of evidence that lead us to the conclusion that this is not what happened:

1. Lack of direct evidence. We'll start with weakest evidence, because as you will no doubt realise absence of evidence is not evidence of absence. However, in this case we have looked and not found, which is a slightly different matter. There is no point in the fossil record were we find evidence for multiple lines of origin, with the possible exception of around the precambrian explosion - although new finds are increasingly supporting the fossil artifact interpretation there.

2. Ontogeny. Ontogeny is the developmental process from egg to offspring. You need to be careful here to avoid Haeckel's mistake of 'Ontogeny recapitulates Phylogeny' which is simply not true but there is no doubt that the Ontogeny of closely related organisms is closer than of less closely related organisms and that there is significant homology between quite distant relatives. For example, the parts of the embryo that go on to form the ear bones in humans (and other mammals) are closely homologous to bits that form part of the jaw in reptiles - not only that but looking at the fossil record of the transition from reptiles to mammals we see that these same parts of the jaw bone in reptiles transition to being the ear bones in mammals.

3. General Homology. If there were multiple sources of origin for life on earth we'd expect to see multiple, differing solutions to certain basic problems, just as we see multiple, differing solutions for things such as flight and vision. We don't. For example, all life on earth uses DNA, almost all of it uses the same coding system for that DNA (IIRC, there are 16 in use, but most only occur in rather obscure single celled organisms - all "higher" life forms use the same one), a very similar system of Hox genes occurs in animals from insects and spiders, to Iguanas and Hippos (Hox genes control the overall body plan, like how many legs and where). The closer the species you're looking at, the more of these similarities you will find: for example, all mammals have the same basic eye design, the same fully-divided hearts, etc or the use of mitochondria among all eukaryotes.

4. The Fossil Record. Although we're far from having a complete historical record of the exact evolutionary path of all life on earth, those part of the record we do have fit very well with the concept of common ancestry and match with the patterns implied by genetics, morphology and ontogeny.

5. Genetics. Comparing the genetics of similar species we find that their genetics do tend to be more similar. Note that this doesn't have to be so, since you can get apparently very similar species with very different genetics (which is explained by convergent evolution, usually backed up by the fossil record and certain features of ontogeny or morphology) so we know that morphological similarity doesn't have to imply genetic similarity. Where genetics gets it best evidence for common ancestry comes from "junk" DNA, faulty genes and mitochondria.

I've put "junk" in quotes because some DNA once labelled as junk has turned out to have useful function and doubtless some of the remainder will also turn out to have meaning. It's called junk DNA because it does not get expressed as genes, and thus proteins. Since junk DNA has no effect on the animal it is not subject to natural selection and thus is simply passed on with mutations. We can estimate the average time between mutations and use this to estimate the total time between changes. By comparing sections of DNA from different species therefor we can estimate the time since they diverged. By doing this with many sections we can improve the accuracy of these estimates. Mitochondrial DNA - since it is passed only through the maternal line - provides a similar clock. Mitochondria is also useful because unlike junk DNA it's pretty much directly comparable between even very different species and thus can be used as a much better indicator.

I've wandered somewhat off point here, haven't I? Going back to common ancestry, junk DNA and mitochondrial DNA provide evidence for common ancestry because we can construct trees of life from the changes in them. Since junk DNA is not used, it seems reasonable to suppose that it will only be similar if it derives from the same original source. This leads us to believe that species with similar junk DNA do indeed share a common ancestor.

The third source I mentioned above is faulty genes. In some species a fault in a gene found in other similar species prevents it from following it's usual function. An example here is the gene which allows most primates to synthesise vitamin C. Humans have a fault in this gene that prevents us from doing this, and thus we get scurvy if we don't eat enough vitamin C. Chimps share this fault - the same error in the same place in the same gene. Since there is no selective reason for this (since the human-chimp ancestor probably ate a lot of fruit like chimps do today, the inability to synthesise vitamin C is not a problem thus why the error was not selected against) we may conclude that the matching error implies a common ancestry.

Now each line of evidence on it's own is not conclusive. It might be that DNA is the only possible coding method (although we know it's not because viruses use RNA) or that Hox genes are the only viable method of body plan structuring, and so on and so forth. But the really convincing thing is not only that there are so many lines of evidence but that they all agree with one another.

Regards,

Mr Jack

 

[Truppenzwei]

Hi Truppenzwei,


Only if you are going to ignore the history and meaning of the term 'species' and used it to simply mean group. We may not be able to give a precise formal definition for the term but we can use it informally in most cases without ambiguity. Incidentally there is a group that already contains house cats and blue whales - placental mammals.

That's kind of my point - first we take life on earth and divide it up according to certain rules which we have made up i.e if it has gills its a fish if it has wings it a bird, but if it's wings are this way instead of that way then it's not a bird it's a bat etc. Once we have divided things up we label them and then come up with theories to explain how all these different things came about and why they are so different.

We could indeed have multiple ancestors that evolved separately according to the mechanisms of evolution.

I never said that the ancestors had evolved - I said that evolution started with them - we agreed not to talk about how life began. If we take a point in time let's call it X and say that that is when reproduction started - or perhaps more correctly the ability to reproduce began - and thus evolution began. Now what the current view of evolution is is that from this point X at which point evolution says there was only one organism that began to reproduce and thus evolve. naff pic here But what if instead of there being just one organism at point X there were many
organisms which began to reproduce and thus evolve nother naff pic here (please don't read too much into length of lines/ number of branches etc I was just being very quick and sloppy in PS)

As has been clearly stated loads of times evolution isn't really about the origins of life - regardless of what the original book was called. So if we instead posit the simple thing that a bunch of organisms with much the same genetic makeup all began reproducing at the same time and thus evolving - given that we have already boiled evolution down to being simply the genetic change in a population over time.

However, such a scenario would be extremely unlikely to produce the situation we have today (depending somewhat on what you suppose those ancestors to be). There are several lines of evidence that lead us to the conclusion that this is not what happened:

1. Lack of direct evidence. We'll start with weakest evidence, because as you will no doubt realise absence of evidence is not evidence of absence. However, in this case we have looked and not found, which is a slightly different matter. There is no point in the fossil record were we find evidence for multiple lines of origin, with the possible exception of around the precambrian explosion - although new finds are increasingly supporting the fossil artifact interpretation there.

Again I would have to disagree here - as I've stated before I've got very grave doubts about how useful the fossil record actually is - because to use the coelocanth example the fossil record had that species extinct but it was still pottering about -it just wasn't ending up in any fossils so how much more life hasn't turned up in the fossil records? Also lets look at how a fossil becomes a fossil - there is no fixed timescale saying it will take this long to become a fossil is there also some of the "earliest" fossils are quite complex, in fact when we get right down to it I would say that a cell is probably one of the most complex things I've ever heard of.

2. Ontogeny. Ontogeny is the developmental process from egg to offspring. You need to be careful here to avoid Haeckel's mistake of 'Ontogeny recapitulates Phylogeny' which is simply not true but there is no doubt that the Ontogeny of closely related organisms is closer than of less closely related organisms and that there is significant homology between quite distant relatives. For example, the parts of the embryo that go on to form the ear bones in humans (and other mammals) are closely homologous to bits that form part of the jaw in reptiles - not only that but looking at the fossil record of the transition from reptiles to mammals we see that these same parts of the jaw bone in reptiles transition to being the ear bones in mammals.

I think that the fact that all life shares common ground rules and that things develop after the fashion of their kind/population/species doesn't require everything to have come from a common ancestor - just similarly made(on the genetic level anyway) ancestors

3. General Homology. If there were multiple sources of origin for life on earth we'd expect to see multiple, differing solutions to certain basic problems, just as we see multiple, differing solutions for things such as flight and vision. We don't. For example, all life on earth uses DNA, almost all of it uses the same coding system for that DNA (IIRC, there are 16 in use, but most only occur in rather obscure single celled organisms - all "higher" life forms use the same one), a very similar system of Hox genes occurs in animals from insects and spiders, to Iguanas and Hippos (Hox genes control the overall body plan, like how many legs and where). The closer the species you're looking at, the more of these similarities you will find: for example, all mammals have the same basic eye design, the same fully-divided hearts, etc or the use of mitochondria among all eukaryotes.

To me this would actually be evidence of similar ancestors then evolution than one common ancestor then evolution which doesn't even account for all the different types of life ie viruses etc. Given that evolution makes no claim for what happened before reproduction started I don't see how it can say it had to be one common ancestor.

4. The Fossil Record. Although we're far from having a complete historical record of the exact evolutionary path of all life on earth, those part of the record we do have fit very well with the concept of common ancestry and match with the patterns implied by genetics, morphology and ontogeny.

Again I'd say the fossil record shows a few brief glimpses of some organisms - nothing more and nothing less

5. Genetics. Comparing the genetics of similar species we find that their genetics do tend to be more similar. Note that this doesn't have to be so, since you can get apparently very similar species with very different genetics (which is explained by convergent evolution, usually backed up by the fossil record and certain features of ontogeny or morphology) so we know that morphological similarity doesn't have to imply genetic similarity. Where genetics gets it best evidence for common ancestry comes from "junk" DNA, faulty genes and mitochondria.

I've put "junk" in quotes because some DNA once labelled as junk has turned out to have useful function and doubtless some of the remainder will also turn out to have meaning. It's called junk DNA because it does not get expressed as genes, and thus proteins. Since junk DNA has no effect on the animal it is not subject to natural selection and thus is simply passed on with mutations. We can estimate the average time between mutations and use this to estimate the total time between changes. By comparing sections of DNA from different species therefor we can estimate the time since they diverged. By doing this with many sections we can improve the accuracy of these estimates. Mitochondrial DNA - since it is passed only through the maternal line - provides a similar clock. Mitochondria is also useful because unlike junk DNA it's pretty much directly comparable between even very different species and thus can be used as a much better indicator.

I've wandered somewhat off point here, haven't I? Going back to common ancestry, junk DNA and mitochondrial DNA provide evidence for common ancestry because we can construct trees of life from the changes in them. Since junk DNA is not used, it seems reasonable to suppose that it will only be similar if it derives from the same original source. This leads us to believe that species with similar junk DNA do indeed share a common ancestor.

The third source I mentioned above is faulty genes. In some species a fault in a gene found in other similar species prevents it from following it's usual function. An example here is the gene which allows most primates to synthesise vitamin C. Humans have a fault in this gene that prevents us from doing this, and thus we get scurvy if we don't eat enough vitamin C. Chimps share this fault - the same error in the same place in the same gene. Since there is no selective reason for this (since the human-chimp ancestor probably ate a lot of fruit like chimps do today, the inability to synthesise vitamin C is not a problem thus why the error was not selected against) we may conclude that the matching error implies a common ancestry.

Again I would say that a bunch of genetically similar ancestors then evolution accounts for this just as well.

Now each line of evidence on it's own is not conclusive. It might be that DNA is the only possible coding method (although we know it's not because viruses use RNA) or that Hox genes are the only viable method of body plan structuring, and so on and so forth. But the really convincing thing is not only that there are so many lines of evidence but that they all agree with one another.

I'd have to say that they don't seem to agree from where I'm sitting. Indeed if we hadn't agreed not to deal with abiogenesis I'd say the evidence pointed more to my theory than the currently popular one. What's more likely - that all this diversity came about because of

a) There was diversity at the start of the evolutionary process.
b) Somehow bacteria made us and horses and fishes and puppies and llamas and pansies and turnips

Now again don't get me wrong Mr Jack - I think that evolution in as much as it means the process of genetic change in a population is a given. It's the grander claims of speciation etc that I think are outwith the provable remit of evolution. I suppose you could say that I think micro-evolution as I've defined it above is true and has been, as far as I can make out pretty convincingly scientifically verified whereas macro-evolution just isn't true and hasn't been anywhere near proved.

Regards
T.

 

[Mr Jack]

Hi Truppenzwei,

I'm off to France to go Snowboarding next week. I will be leaving early tomorrow morning so I probably won't be able to post any more answers until a week on Monday. Sorry.

That's kind of my point - first we take life on earth and divide it up according to certain rules which we have made up i.e if it has gills its a fish if it has wings it a bird, but if it's wings are this way instead of that way then it's not a bird it's a bat etc. Once we have divided things up we label them and then come up with theories to explain how all these different things came about and why they are so different.

Species is simply terminology, it doesn't matter that much. What is unambiguously true is that there are different kinds of life on earth, and some of them are more similar to each other than others. The species/genus/family/etc. categorisation system is simply a convenient and useful way of looking at them.

The very fact that we can arrange all life into neat hierarchical classifications is evidence for evolution. There so inherent reason it has to be so. There's no fundamental reason that, for example, the number of holes in a creature's skull should match with them being cold blooded egg-layers or that all cold-blooded egg-layers should lack fur.

Historical evolution study is not, in any way, dependent on how we choose to divide life up into convenient pots. In fact, it's increasingly the other way round, since cladistics is now an accepted reason for changing how we classify a life form. There also a group of scientists pushing to abandon the existing system altogether and instead use a pure cladistics approach.

I never said that the ancestors had evolved - I said that evolution started with them

That's what I meant, perhaps if I'd put a 'then' in there it would have been clearer.

Again I would have to disagree here - as I've stated before I've got very grave doubts about how useful the fossil record actually is - because to use the coelocanth example the fossil record had that species extinct but it was still pottering about -it just wasn't ending up in any fossils so how much more life hasn't turned up in the fossil records?

Quite a lot of it; there are whole branches of life we have virtually no fossil record for - the Australian Monotremes, for example. The fossil record is decidedly patchy. However, we do have have literally millions of fossils from around the world. These fossils all fit with the common ancestor theory of evolution.

Also lets look at how a fossil becomes a fossil - there is no fixed timescale saying it will take this long to become a fossil is there also some of the "earliest" fossils are quite complex, in fact when we get right down to it I would say that a cell is probably one of the most complex things I've ever heard of.

Certainly is. Trouble is single celled organisms don't exactly leave fossils, so we have pretty much no idea what happened before around 800 million years ago excepting a few rare finds that still tell us very little about the nature of the life involved (things like Devil's Causeway in Ireland), even then have only the rarest of finds to go on. It isn't really until life started developing hard parts that we get any kind of useful record and, of course, the older the fossils the rarer, harder to find and less likely to be complete they are.

So, yes, there could have been multiple common ancestors that appeared before we start getting a decent fossil record and the fossil record can't tell us any different but that doesn't work for things like tortoises, horses, ducks and chimps because we have enough of a fossil record to tie all of these creatures together.

I think that the fact that all life shares common ground rules and that things develop after the fashion of their kind/population/species doesn't require everything to have come from a common ancestor - just similarly made(on the genetic level anyway) ancestors

No, it doesn't require it. For pretty much anything in Science there is more than one possible explanation, it's a matter of finding an explanation that fits all the data and involves the fewest co-incidences. The evidence, for example, that horses and zebras share a common ancestor is stronger than the evidence that horses and monkeys do and stronger than the evidence that horses and bacteria do. What level of different ancestors are you talking about? A different ancestor for mammals and bacteria? A different ancestor for equines and monkeys? A different ancestor for horses and zebras?

The big question for you to answer is why these hypothetical multiple ancestors are so very similarly made?

To me this would actually be evidence of similar ancestors then evolution than one common ancestor then evolution which doesn't even account for all the different types of life ie viruses etc. Given that evolution makes no claim for what happened before reproduction started I don't see how it can say it had to be one common ancestor.

How so? The pattern of similarity we see is exactly that we would expect if all life evolved from a common ancestor. We see similarities across all life, and then hierarchically arranged similarities which match up with evolutionary trees of life created from other lines of evidence. If, for example, equids and felines evolved from separate common ancestors why do they both share features such as a crossing of the airways, the crossing of genital and urinary tracts, a fully divided heart, a placental approach to live birth, mammary glands with nipples, similar eye design, the same ear bones and so on?

Why don't these features appear in other groups of animals?

I'm not sure of the relevance of your point about viruses. How are they relevant to whether the rest of life evolved from a common ancestor? You must understand that viruses don't leave us any record at all from which they can deduce their ancestry either way.

Again I'd say the fossil record shows a few brief glimpses of some organisms - nothing more and nothing less

That's true, but as I said above, we do have literally millions of fossils and they all match with the common ancestor theory. If the common ancestor theory is incorrect, why is this so? And why don't we find any direct evidence for multiple ancestors?

Again I would say that a bunch of genetically similar ancestors then evolution accounts for this just as well.

The big question again occurs - why are these ancestors genetically similar? Why does their genetic similarity line up so well with other lines of evidence? How on earth do you account for similarity in junk DNA and faulty genes with genetically similar ancestors? Why does the independent evidence from Mitochondrial DNA line up with the main body of genetic evidence?

Common ancestry answers all of these questions. Multiple similar ancestors can't answer any of them.

I'd have to say that they don't seem to agree from where I'm sitting.

You'll have to be more specific. Where do the lines of evidence I've presented disagree with each other?

a) There was diversity at the start of the evolutionary process.
b) Somehow bacteria made us and horses and fishes and puppies and llamas and pansies and turnips

There's a fundamental difference between a) and b) - we have evidence and mechanism for b), and neither for a).

I suppose you could say that I think micro-evolution as I've defined it above is true and has been, as far as I can make out pretty convincingly scientifically verified whereas macro-evolution just isn't true and hasn't been anywhere near proved.

You can't use use your own definition of macro-evolution because you won't accept any definition of speciation that would allow macro-evolution to occur. If you do accept a definition of speciation (for example, the BSC) then macro-evolution as defined by you has been observed both in the laboratory and in the wild (see link in my last post).

Cheers,

Mr. Jack

 

[Truppenzwei]

Actually that's good timing Mr Jack because I've just been project bombed by my boss so would have been hard pushed to deal with answering stuff next week as well.

You enjoy your trip and "luge a pipe" (or whatever it is snowboarders do) for me

:wave2:

 

[Mr Jack]

For me, I mostly fall over. 'Twas my first time up a mountain, having learnt in a snow dome.

Anyway, I'm back and have managed to not break anything so shall we pick up where we left off?

 

[Truppenzwei]

Heya Mr Jack,

Nice to have you back in one piece. I've taken some time and gone through a lot of the references you gave and dug into the whole speciation thing and I found a definition that I feel I can agree with that in essence said a population that cannot reproduce with it's parent population is a new species (very paraphrased) but I feel more confident that that is a more telling definition than "this type of finch is a different species to this one because there beaks are different thicknesses" it was this kind of speciation event that I was dubious about but I totally accept the definition I've mangled above.

Now using that as the basis for speciation then I could agreee that speciation occurs - however it only seems to occur within what I would previously of thought of as a species ie. Mosquitos I thought of mosquitos as being the species but it is some other word instead.

However even given this speciation within a tree - e.g. equine or canine I don't see the evidence that takes us back to the SCA - Perhaps if you could provide some references for the evidence that shows how the horse and dog (or apes and bats etc) are descended from the same ancestor that might help clear up some of my confusion.

Because at the moment I see no reason why given a diverse set of common ancestors at the point of reproduction beginning we wouldn't end up with exactly the situation we have today. And to be honest I see no evidence to disprove the theory either. Please note - I'm making no claims to where these ancestors came from as that is outwith the purview of a discussion on evolution.

 

[Mr Jack]

Hi Truppenzwei,

Now using that as the basis for speciation then I could agreee that speciation occurs - however it only seems to occur within what I would previously of thought of as a species ie. Mosquitos I thought of mosquitos as being the species but it is some other word instead.

Indeed so, and that is exactly what we should expect if evolution is true. Evolution is primarily a gradual process of accumulated small changes. Given the time scale on which we have been able to observe these processes we shouldn't expect to see any radical changes occurring. Your statement is analogous to measuring a tree in the morning, then again in the afternoon and concluding it can't be growing by cell division because it is the same height in the afternoon as it was in the morning.

Because at the moment I see no reason why given a diverse set of common ancestors at the point of reproduction beginning we wouldn't end up with exactly the situation we have today. And to be honest I see no evidence to disprove the theory either.

Hmm, I'd like to know your response to the questions I posed in my last proper post. I find the arguments from homology and genetic compelling - what is it about them that you find lacking?

Please note - I'm making no claims to where these ancestors came from as that is outwith the purview of a discussion on evolution.

Of course. However, I do need to know something about what it is you are thinking if I am to argue cogently as to why SCA should be considered a more convincing explanation.

Rather than going straight to establishing a SCA for two distinct and extant groups I'd like to start by looking at the fossil record of evolution for whales, at the evolution from this to this. The full story in some detail can be found here, although that source is rather lacking in actual fossil photos, so you may want to visit here as well.

I've chosen this example for two reasons: firstly, it's one of the ones for which the fossil record is particularly good and, secondly, because it shows a rather radical change from a wolf-sized, terrestrial tetrapod to a huge, legless, ocean going whale. The important point I wish draw your attention to here is the convergence of separate lines of evidence. If, in fact, Sinonyx is not an ancestor (or close relation of the ancestor of, more precisely) modern cetaceans why is it that these evidential lines converge? Why is it that we can locate such a series of fossils documenting the evolutionary history of whales?

Now, to bring it back to the question you asked, the fact is that we do not have a nice fossil record like this one for all mammals. I doubt I can locate a neat sequence of fossils tracing both horses and dogs back to their common ancestor in a way that would convince you (horses have a very good record going back about 60 million years, but I couldn't locate a similar record for canidae and even if I had the two evolved from ancestors who had already diverged by that time). However, if you look at the whale evidence you can see a well documented case linking very dissimilar animals so we can know that such changes are possible.

I have tried throughout this discussion to present multiple sources of evidence for each evolutionary claim. I think this is the key point about evolution. There is no single piece of smoking gun evidence for evolution that should convince you beyond reasonable doubt but rather a large, coherent and consistent body of evidence and confirmed predictions.

For a sufficiently devious set up of common ancestors there is no possible test we can do that will prove that it didn't happen - this is essentially a re-telling of Descartes's demon doubt - but if we look at the evidence we have and try to construct the most parsimonious (containing the least co-incidences) and plausible explanation we are inevitably drawn to a SCA interpretation for all higher life. Why else would all vertebrates use the same spine design? Have the same crossing of the genital and urinary tracts and the same eye design?

The fossil record can't prove SCA but it can show convergence in time. The whale ancestor Sinonyx is more similar to ancestral horses than a horse is to a whale, both converge towards earlier mammals, then protomammals and what appear to be reptile-mammal transitionals. This pattern is exactly what we should expect from SCA but has no explanation under MCA. Now you could argue that we're simply looking for similar animals and then lining them up like they're related when, in fact, they're not (which, wouldn't IMO be a fair criticism but I'll let it stand for now) but then you are left with trying to explain why the evidence from genetic sources matches that from the fossil record, and why ontogeny confirms them both.

I've been talking thus far about SCA among higher animals. Sadly the evidence slips rather as we move away from them. There are no fossil indicating when insects emerged as a separate group, or how. No records proving a link between Archae and Eucaryotes and no records indicating when plants and animals diverged. Here we must rely on homology among basic systems (e.g. DNA) and extrapolation - essentially having satisfied ourselves that all higher animals share a common ancestor it seems most reasonable to assume that, in the absence of other evidence, we share our ancestors. Other explanations must make unreasonable appeals to chance.

Cheers,

Mr. Jack.

(As an aside, in an earlier post you mentioned abiogenesis as being off-topic, I would be quite happy to discuss this with you later on providing it understood that it is a separate subject)

 

[Truppenzwei]

HI Mr Jack,

Sorry for the delay - snowed under at work at the moment. I'll try and sit down on Saturday and respond.

 

[Mr Jack]

Hi Truppenzwei,

I'd rather have a thought out response later than a quick response now so, please, take your time.

Cheers,

Mr. Jack.

 

[Truppenzwei]

Hi Mr. Jack - sorry for the delay but work is frantic at the moment - I am considering your questions and have ordered a couple of books on evolution just to make sure that I've got things right. I will hopefully have a decent response in the next day or so if work calms down a bit.

 

[Mr Jack]

Hey Truppenzwei,

What's the state of play? Are we to continue with this?