How can scientists possibly know ... ?? An open exploration thread

[holdon]

Linnean classification:

rosids--sub-class of eudicotyledons (a class)
Rosales--order
Rosaceae--family
Rosa--genus

The NCBI taxonomy browser lists over 100 defined species of plant in the genus Rosa.

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

To see the list type Rosa in the search engine. Note that species are listed along the left margin and varieties and sub-species are in an indented list under the species they are varieties or sub-species of.

To see a list of tulip species type Tulipa in the search engine.

You're making it only more difficult for yourself. Because, if you consider the genus rather than the species, and you want to make a new genus, then you're are in for even more trouble. Yes there are different rosa species and different tulip species. But I bet the common reader would not recognize the majority of them as such. And that's what I am talking about: the common garden variety. You seem to claim new species arise all the time. Which tulip or rosa species by the way is a new one?

No, I do not. By species I mean a population that is reproductively isolated from its ancestral population.

No, that would rather be a subspecies.

Some species of polyploid roses exhibit this characteristic of reproductive isolation.

But that is because they're "messed up", not in their natural left alone state. And therefore it is incorrect to call them a new species.

Actually tulips are monocotyledons, which puts them in an entirely different Linnean class than roses. A rose-tulip hybrid is as likely as one of a sparrow with a minnow.

Well, of course. But what about your new species of roses? Which one has occured out of other species in recent memory (this to qualify that it did indeed occur)?

Both nature and breeders produce new varieties. Breeders have to take care that their varieties do not spontaneously hybridize because they are not reproductively isolated from others of the same species.

But hybridization is not a "new species". You seem to forget that that is what we're talking about here. Now, if you "re-arrange" the definition of "species", then of course you can have any result you like.

 

[gluadys]

Evolutionists in recent years have re-defined the word "species" as you have used it here, because when used in this way, it is possible to demonstrate the rise of new "species."

Got a source for this accusation?

It is certainly true that the concept of species is a matter of controversy and that various schemes have been proposed and considered. While the biological species concept is useful in many situations, there are others where it is not applicable. But no other proposed system is applicable in all cases either.

In fact, no one system for recognizing species is being used universally.

It is also the case that using the biological species concept has in some cases reduced the number of recognized species. In Origin of Species, chapter one, Darwin mentions one taxonomist of his day who classified the domestic sheep of Great Britain as eleven different species.

There is just as much, if not more difficulty distinguishing species from sub-species and varieties from a baramin perspective as from an evolutionary perspective.

As for the roses---how many of these were recognized and named as species before 1859?

But this definition totally breaks down if the isolated populations are again allowed to mix, for then the new "species" disappears.

That can be the case in allopatric situations where segments of the population are temporarily cut off geographically from the rest of the species. If, when they get together again, they mix, it indicates that geographical isolation in this case did not produce reproductive isolation.

OTOH we also have examples of sympatric speciation, where reproductive isolation occurred even without geographic isolation. And we have examples where reproductive isolation was a consequence of geographic isolation.

If you define a species by reproductive isolation, we have seen the emergence of new species---species which do not disappear when brought together again with the parent species.

And I maintain that a change in the predominant characteristic of a species is not evolution.

Then you are not using a standard definition of evolution.

To validly demonstrate that evolution is physically possible, it would necessary to demonstrate a situation in which new genetic material began to exist, and that this material conferred a unequivocal benefit to those offspring that inherited it.

Define "new" and "unequivocal". Does a gene duplication count as "new"? Does it count as new if it produces a variation in a species trait?

Does "unequivocal" mean "in all foreseeable circumstances"? If so, that is a red herring as no trait is beneficial in all circumstances. Melanism was beneficial to the moth when industry was fouling the environment, but became detrimental when pollution controls were established.

This has not been done, because the overriding assumption that evolution is indeed factual makes almost everyone who calls themselves scientists to simply assume that new genetic material began to exist at every stage along the evolutionary trail.

Actually, that is not the case. In fact, it has been demonstrated that new genetic material often occurs well before circumstances arise in which it is beneficial and begins to be selected. Inheritance keeps it in the gene pool while it is neutral. Selection makes it predominant when environmental pressures make it adaptive. So the "new" material was not "new" when evolution changed its frequency of occurrence.

 

[holdon]

Not only that. We also know that nobody purchased anything for $0.90 or $1.37 or any price that was not a multiple of $0.60.



That would be a faulty conclusion, but it is not the conclusion shernren was getting at. The correct conclusion is that all prices per sales unit were $0.60 or multiples of $0.60. Whether the sales unit was a single candy bar, a package of 8 toffee candies or a case of 100 Tic-Tacs is not relevant. Because there is no sales unit of one Tic-tac or one toffee in the package.

So, how do you know exactly what the buyer bought? Answer: you don't. And it has nothing to do with math. And that is the whole argument. We deduct to the best of our abilities, from what we observe. But there is always a possibility that we're wrong. That's why science exists: to continuously look for "better" answers. Otherwise we would have known everything a long time ago.....

 

[Mallon]

Like I said: it doesn't prove it..... But I believe it. Science is just like that: a belief.

"Proof" is beyond the scientific methodology. Science is capable of rejecting hypotheses, but ultimately, science cannot provide "proof" of anything because it cannot account for every universal variable. Proof is for math.
What science is capable of is providing support for a theory when all hypotheses to the contrary have been rejected. You can call this a "belief" if it makes you feel better, but "belief" is typically a word reserved for that which cannot be seen. And you may equally regard Occam's razor as nothing more than an assumption, which is true, but as you demonstrated earlier, even you rely on Occam's razor when you find snow on the ground in the morning. So why not be consistent and apply the same logic to the charge of an electron?

I like the "I'am using the same as scientist". Are you in need of some credence?

I am a scientist. And I am using the same textbook definition of evolution that all other scientists use (change in allele frequencies through time leading to reproductively isolated populations, etc.). I am not using your definition of evolution, whereby coeval species are able to transform into one another. That's a strawman.

No, I didn't say they can at all. What's wrong with your reading skills? And what exactly does the theory of evolution suggest? Define a species, and then maybe we can test the research against that....

If you're genuinely interested in how evolution works, I would direct you to this site for beginners:
http://evolution.berkeley.edu/
Particularly the section called "What is evolution and how does it work?"

If you're interested in discussing the papers cited earlier, working under a particular species definition, then I suggest we use the biological species definition, as this is the common definition used by biologists. If you do not already know what the biological species definition is, it is this (from Wikipedia):

"A set of actually or potentially interbreeding populations. This is generally a useful formulation for scientists working with living examples of the higher taxa like mammals, fish, and birds, but meaningless for organisms that do not reproduce sexually. It does not distinguish between the theoretical possibility of interbreeding and the actual likelihood of gene flow between populations and is thus impractical in instances of allopatric (geographically isolated) populations. The results of breeding experiments done in artificial conditions may or may not reflect what would happen if the same organisms encountered each other in the wild, making it difficult to gauge whether or not the results of such experiments are meaningful in reference to natural populations."

Let me know which paper you're interested in discussing (preferably a recent one, since they're easier to get as pdf files), and I'll see if I can get a hold of it.

 

[holdon]

In fact, it has been demonstrated that new genetic material often occurs well before circumstances arise in which it is beneficial and begins to be selected.

Ah, this is nice too. New genetic material often occurs before it is beneficial??? Who and how does one determine that? Of course I can understand the wish to be father of the thought.
But New genetic material is detrimental in 99% of the cases..... and will get eliminated.

 

[Mallon]

Polyploidy is only an erroneous multiplication of existing genetic material, and hybridization is nothing more or less than selective breeding.

"Erroneous"? In what way?
As discussed in the links I provided earlier (and by gluadys), polyploidy often leads to reproductive isolation, whereby the daughter population is no longer able to breed with the parent population. This has been demonstrated in the Salsify plant, for example. It is this genetic isolation that ultimately leads to speciation. This is well-accepted, 1-year biology. How is it wrong?
Hybrid speciation, though rare, occurs in nature also. It is the product of interbreeding between two closely related, but geographically isolated, species. The Mariana Mallard duck is an (extinct) example of a species produced via hybridization.

And selection most absolutely has nothing to do with the development of new genetic material.

You're right. Selection acts on genotypic variation to produce speciation. It does not create "new genetic material" on its own. I agree.
You're equating speciation with mutation, though, which is wrong.

The earliest "demonstration" of evolution in progress that I personally remember is a butterfly population in England. Supposedly, in earlier days the population was 90% white. But afterward, when the industrial revolution had turned the countryside black, that population was found to be 90% black.
But this demonstration wholly neglected that fact that the black variant already existed when the supposed demonstration began.

I think you misunderstood the experiment (involving peppered moths, not butterflies).
The experiment demonstrated the power of natural selection to favour particular phenotypes in just a few generations. It did not seek to explain how those colour variants came about (mutation causes variation). You can read more about the experiment here:
http://www.millerandlevine.com/km/evol/Moths/moths.html

What was actually demonstrated, supposing the alleged facts were indeed correct, was nothing more than natural selection. But the evolutionists hailed it as a proof of evolution!

It was proof of the mechanism of evolution, yes.

Your assertion is really an admission that the scientific method cannot be applied to evolutionary theory. All of the fields you mentioned (even much of ecology) are connected with the false premise that evolution is science.

But the scientific method CAN be applied to evolutionary theory. The scientific method is illustrated here:

Note that nowhere is a control specified. Controls are great to have, and add credibility to one's explanation of the results, but as I stated earlier, they are not always possible. This doesn't make palaeontology, ecology, geology, or astronomy unscientific.

I well remember an article that was published in the (peer reviewed) Journal of Geology. The article was about human-like footprints that occurred in Cretaceous strata over a wide area in the eastern United States. The article ended with a statement to the effect that:
But such information is not only ignored, it is often actively suppressed. Adherents of evolutionary theory have gone so far as to go to court to prevent excavation (on private property) of fossil sites where such footprints have been observed.

I doubt very much that such an article was published in the Journal of Geology. Are you sure you aren't thinking about one of the YEC magazines? Perhaps you can cite the article you were referring to?
For what it's worth, even Answers in Genesis recognizes that those supposed human footprints were just artifacts of erosion:
http://www.answersingenesis.org/home/area/faq/dont_use.asp
(They also admit to speciation.)

In geology, we were taught that the geological record showed gradual changes. But upon examination of the data the same professors presented, it became obvious that the record actually showed a long series of stable ecosystems that suddenly appeared, flourished virtually unchanged for long periods of time, and then suddenly vanished, only to be suddenly replaced by a different stable ecosystem.
So the alleged continuum simply does not exist.

The fossil record does show gradual change, when the resolution is fine enough. We can see this in both the invertebrate and vertebrate record. I can provide you with papers, if you would like, although a picture speaks a thousand words:

Heck, I just published on a new transitional species of mosasaur in the Canadian Journal of Earth Science last August. And my supervisor has a paper in press describing a new transitional species of fossil frog. (Keep an eye out!)

(Out of curiosity, how long has it been since you were last in school, Biblewriter? An awful lot of new data/fossils have come to light in the last 30 years.)

 

[holdon]

"Proof" is beyond the scientific methodology. Science is capable of rejecting hypotheses, but ultimately, science cannot provide "proof" of anything because it cannot account for every universal variable. Proof is for math.
What science is capable of is providing support for a theory when all hypotheses to the contrary have been rejected. You can call this a "belief" if it makes you feel better, but "belief" is typically a word reserved for that which cannot be seen. And you may equally regard Occam's razor as nothing more than an assumption, which is true, but as you demonstrated earlier, even you rely on Occam's razor when you find snow on the ground in the morning. So why not be consistent and apply the same logic to the charge of an electron?

But I do, all while keeping in mind I might be wrong, and the razor could cut yet closer....
But we don't find that often in popular science: they know it all, and it can't be moved.

I am a scientist. And I am using the same textbook definition of evolution that all other scientists use (change in allele frequencies through time leading to reproductively isolated populations, etc.). I am not using your definition of evolution, whereby coeval species are able to transform into one another. That's a strawman.

Ok, good to know. So, what's your explanation for the progressive evolution into new species? (if that did indeed happen)

Let me know which paper you're interested in discussing (preferably a recent one, since they're easier to get as pdf files), and I'll see if I can get a hold of it.

Give me link if you want. I may not have a whole lot of time for this, but we can see.

 

[gluadys]

So, how do you know exactly what the buyer bought? Answer: you don't.

Correct. I don't. And I don't need to. The math alone tells me that every unit of sale was priced either at $0.60 or a multiple thereof. What those units of sale consisted of is irrelevant.

 

[gluadys]

Ah, this is nice too. New genetic material often occurs before it is beneficial??? Who and how does one determine that? Of course I can understand the wish to be father of the thought.

I forget which thread it was in, but shernren recently posted the experiment that proved bacterial resistance to antibiotics existed the population before exposure to the antibiotic. IOW before it was beneficial to have that characteristic. Maybe he can post a link to it for you.

But New genetic material is detrimental in 99% of the cases..... and will get eliminated.

Incorrect. Most mutations are neither beneficial nor detrimental. Of the small minority that are not neutral, most are detrimental.

It is also not always the case that detrimental mutations will get eliminated. It depends on how detrimental and on how strong the selective pressure is. (That is perhaps a tautology. The selective pressure determines how detrimental it is.) The fact is that most organisms get by fine with some detrimental traits. So they don't get eliminated.

 

[Mallon]

But we don't find that often in popular science: they know it all, and it can't be moved.

The fact that we do not think the same about the universe today that we did 100 years ago is obvious testimony against this falsehood.
The only people who cannot be moved are those who abstain from science and hold to religious dogma. Many YECs pride themselves on this fact (just read the anti-evolution subforum).

Ok, good to know. So, what's your explanation for the progressive evolution into new species? (if that did indeed happen)

There are many mechanisms that lead to speciation, the most common being mutation inducing variation, leading to different levels of fitness, and differential reproduction.

Give me link if you want. I may not have a whole lot of time for this, but we can see.

I asked you to provide me with the citation of a paper you wanted to discuss (see posts 18 and 26 for references), and I said would see if I could track it down. It's your choice. You can pick a short one, if you like, given your lack of time.

 

[shernren]

So, how do you know exactly what the buyer bought? Answer: you don't. And it has nothing to do with math. And that is the whole argument. We deduct to the best of our abilities, from what we observe. But there is always a possibility that we're wrong. That's why science exists: to continuously look for "better" answers. Otherwise we would have known everything a long time ago.....

You're absolutely right. We have no idea what the buyers bought.

But we do know that after having received, say, 1,000 receipts, all of them in multiples of $0.60, the chance that any subunits of say $0.20 or $0.30 are being sold is pretty close to zero. Exactly zero? Nopes. There is always the slim chance that sheer luck (or a conniving shopkeeper) could've arranged it so that, say, every sale actually consists of pairs of $0.30 lollies.

But that wouldn't change some hypotheses. For example, I predict that if you enter the shop with a single 5c coin, you will still have that coin on you when you come out. Whether the shop is selling $0.60 lollies, or pairs of $0.30 lollies that still holds. And if for some bizarre reason I was allowed to take the 5c coins of anybody who came out of the shop, I'd get your coin whichever theory I believed.

In the same way, the charge on an electron has been measurably tested. We can write equations that use the charge of an electron (in quantum mechanics, for example) and be confident that the sums will turn out correct: the very fact that your computer works is testament to that. Does that tell us what an electron is? Not really, no. But it allows us to stick a label onto an electron that tells us what it will do under certain conditions with amazing accuracy.

That be science.

Ah, this is nice too. New genetic material often occurs before it is beneficial??? Who and how does one determine that? Of course I can understand the wish to be father of the thought.

The Lederberg experiments: http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml

But New genetic material is detrimental in 99% of the cases..... and will get eliminated.

Not really. With bacteria, for example:

Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these genetic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.
​

(emphasis added) http://www.ncbi.nlm.nih.gov/sites/en...t_uids=9332013

 

[holdon]

Incorrect. Most mutations are neither beneficial nor detrimental. Of the small minority that are not neutral, most are detrimental.

Ok, those "neutral" are the unexpressed mutations. I can agree with that.

It is also not always the case that detrimental mutations will get eliminated. It depends on how detrimental and on how strong the selective pressure is. (That is perhaps a tautology. The selective pressure determines how detrimental it is.) The fact is that most organisms get by fine with some detrimental traits. So they don't get eliminated.

Well, it depends how you determine "detrimental" of course, or "getting by fine".

 

[holdon]

You're absolutely right. We have no idea what the buyers bought.

But we do know that after having received, say, 1,000 receipts, all of them in multiples of $0.60, the chance that any subunits of say $0.20 or $0.30 are being sold is pretty close to zero. Exactly zero? Nopes. There is always the slim chance that sheer luck (or a conniving shopkeeper) could've arranged it so that, say, every sale actually consists of pairs of $0.30 lollies.

And that's about all you can conclude from there.

But that wouldn't change some hypotheses. For example, I predict that if you enter the shop with a single 5c coin, you will still have that coin on you when you come out. Whether the shop is selling $0.60 lollies, or pairs of $0.30 lollies that still holds. And if for some bizarre reason I was allowed to take the 5c coins of anybody who came out of the shop, I'd get your coin whichever theory I believed.

Sure.

In the same way, the charge on an electron has been measurably tested. We can write equations that use the charge of an electron (in quantum mechanics, for example) and be confident that the sums will turn out correct: the very fact that your computer works is testament to that. Does that tell us what an electron is? Not really, no. But it allows us to stick a label onto an electron that tells us what it will do under certain conditions with amazing accuracy.

And you're right. But there is always the possibility (especially in quantum mechanics) that something else is lurking behind that first lollie.... perhaps a second lollie? You can call both together a lollie, but that wouldn't be entirely accurate.

That be science.



The Lederberg experiments: http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml





Not really. With bacteria, for example:

Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these genetic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.​

(emphasis added) http://www.ncbi.nlm.nih.gov/sites/en...t_uids=9332013

And who determines here what is beneficial and what is not? On the face of it resistance to a certain antibiotic may be beneficial (as it prevents the majority of that population from dying), but who is to say what other good aspects might have been sacrificed for that.
We don't know all that. And therefore we see these people jumping to conclusions based on just one aspect they observed.....

 

[holdon]

The fact that we do not think the same about the universe today that we did 100 years ago is obvious testimony against this falsehood.

What??? I still see the same pictures and stories in today's textbooks: there is no evolution on that level. And I said: Popular Science. I am well aware there is the serious kind too, that in general doesn't make such bold statements as to what they know.

The only people who cannot be moved are those who abstain from science and hold to religious dogma. Many YECs pride themselves on this fact (just read the anti-evolution subforum).

Ah, but my religious dogma rests on Revelation. Revelation from God. And that's what I believe. A scientist believes his test tubes and what not and has to, but still cannot be sure that what he observes is the reality. In theology we believe God, and He must be right.

There are many mechanisms that lead to speciation, the most common being mutation inducing variation, leading to different levels of fitness, and differential reproduction.

Yes, of course, if you want to see it that way. Give me new species please.


I asked you to provide me with the citation of a paper you wanted to discuss (see posts 18 and 26 for references), and I said would see if I could track it down. It's your choice. You can pick a short one, if you like, given your lack of time.[/quote] My goodness, how do I know which is a short one in the first place. No thanks, going to bed.

 

[Mallon]

What??? I still see the same pictures and stories in today's textbooks: there is no evolution on that level. And I said: Popular Science. I am well aware there is the serious kind too, that in general doesn't make such bold statements as to what they know.

What pictures are you referring to? Please be specific.
If you're referring to Haeckel's embryos, these are being replaced:
http://www.millerandlevine.com/km/evol/embryos/Haeckel.html

Ah, but my religious dogma rests on Revelation. Revelation from God. And that's what I believe. A scientist believes his test tubes and what not and has to, but still cannot be sure that what he observes is the reality. In theology we believe God, and He must be right.

So we agree that you believe in your fallible interpretation of God's written revelation, which you do not subject to external testing.
This is in contrast to science, which is also fallible, but subject to correction given new evidence.

Yes, of course, if you want to see it that way. Give me new species please.

Again, these have been provided in the references cited to you earlier, which I continue to encourage you to check out. If you're looking for specific epithets, here are a few: Petroica multicolor, Larus gulls, Phylloscopus trochiloides, Xenopus laevis (got a few of these frogs in my lab). There are many more, if you're willing to put in the research.
So, we have provided you with several mechanisms of speciation, both in controlled lab environments and in nature, identifying those species involved, and supported our statements with cited literature. If you're willing to reciprocate the favour, perhaps you could explain the mechanism that you think prevents populations from becoming reproductively isolated, and thereby speciating.

My goodness, how do I know which is a short one in the first place. No thanks, going to bed.

Because, had you bothered to check, you would have noticed that the page numbers were given.

 

[gluadys]

Ok, those "neutral" are the unexpressed mutations. I can agree with that.

Mutations can be expressed and still be neutral in regard to fitness. Is white or red a more beneficial colour for a rose?

Well, it depends how you determine "detrimental" of course, or "getting by fine".

Getting by fine means surviving and reproducing healthy, viable offspring. People do this even when they have detrimental traits like shortsightedness, loss of hearing, a tendency to obesity and various other detrimental characteristics. They would be better off without these problems, but they still manage to mate and produce children.

Happens in other species too.

 

[gluadys]

And who determines here what is beneficial and what is not? On the face of it resistance to a certain antibiotic may be beneficial (as it prevents the majority of that population from dying), but who is to say what other good aspects might have been sacrificed for that.

That's the point. Most characteristics cannot be beneficial in all circumstances. An adaptation to heat will not help if the climate turns cold. Excellent eyesight is no benefit if one takes up inhabiting caves.

There is always something sacrificed because adaptation in one direction always means maladaptation from another perspective.

That is why a demand for "unequivocal" benefit is unrealistic. There is no such thing as an unequivocal benefit because the better adapted a species is to one environment the less well it is adapted to any other environment.

 

[holdon]

So we agree that you believe in your fallible interpretation of God's written revelation, which you do not subject to external testing.

Hey, if it is God who is talking, who am I to question that? Of course my interpretation may be fallible, but He is not.

This is in contrast to science, which is also fallible, but subject to correction given new evidence.

Science is not infallible, because it is human. Humans bring their own views and interpretation into it.

Again, these have been provided in the references cited to you earlier, which I continue to encourage you to check out. If you're looking for specific epithets, here are a few: Petroica multicolor, Larus gulls, Phylloscopus trochiloides, Xenopus laevis (got a few of these frogs in my lab). There are many more, if you're willing to put in the research.

I was hoping for new species. Alas, I didn't, as I googled these that you mentioned.

 

[holdon]

Mutations can be expressed and still be neutral in regard to fitness. Is white or red a more beneficial colour for a rose?

Your "fitness" argument is subjective and arbitrary. White roses may indeed be less fit as they are more susceptible to thrips and other diseases.

Getting by fine means surviving and reproducing healthy, viable offspring. People do this even when they have detrimental traits like shortsightedness, loss of hearing, a tendency to obesity and various other detrimental characteristics. They would be better off without these problems, but they still manage to mate and produce children.

Happens in other species too.

Yes, but obese people for instance may have children, but are have a lesser survival chance than non-obese. So, over time, per the survival of the fittest theory, they would tend to disappear in the normal population. So, your perspective of getting by is again colored by your opinion on the matter, hardly by scientific evidence. And so it must be. Everybody interprets depending on the way they were taught. Objectivity it is not.

 

[holdon]

That's the point. Most characteristics cannot be beneficial in all circumstances. An adaptation to heat will not help if the climate turns cold. Excellent eyesight is no benefit if one takes up inhabiting caves.

There is always something sacrificed because adaptation in one direction always means maladaptation from another perspective.

That is why a demand for "unequivocal" benefit is unrealistic. There is no such thing as an unequivocal benefit because the better adapted a species is to one environment the less well it is adapted to any other environment.

I agree. All it is adaptation within a species to pressures of various kinds. This does not explain new species occuring, if they do.