That paper was simply wrong. Not the sequence of the gene, which was right as far as I know, but in the interpretation of what they found. The authors assumed that any sites where the guinea pig sequence and the human sequence agreed, and both disagreed with the rat sequence, represented convergent mutations in human and guinea pig. It seems not to have occurred to them that the gene was also mutating in the rat lineage; almost all of these sites represent those mutations. If you compare with a fourth species (I used cow, I think, when I looked quite a few years ago), you’ll find that that species agrees with human and guinea pig too.
That’s what happens when you publish conclusions about molecular evolution in a nutrition journal: the reviewers are not going to spot obvious problems.
1)the evolutionists also assume that the rat sequence is the sequence that changed. but if we not assume that the evolution is true- then the rat sequence represent the original one.
2)mouse also share this mutations. so according to this logic we can never know when is the result of convergent and when it isnt.
3)the exon loss is the same.
4)we have cases with real convergent even according to any evolutionists. so even if we ignore the gulo case we have a lot other.
Your goal was to test a prediction of evolution. That means you have to test the actual test of evolution, not an incorrect prediction made by a nutritionist who didn’t understand evolution adequately.
What mutations are also shared by mouse? What study are you looking at? Which mutations are convergent is generally quite clear when you’ve densely sampled the phylogenetic tree.
The exon loss isn’t at all the same. Guinea pigs have lost exons 1, 5 and part of 6. Humans have lost all of 1, 2, 3, 5, 6, 8 and 11 (and parts of other exons). Since humans are missing most of the gene, it’s not very surprising that another species’ lost exons will overlap those of humans.
In order to really test the evolutionary prediction, you have to look at the specific mutations present in humans and guinea pigs. You can find a helpful list in this paper: "Inactivation dates of human and guinea pig vitamin C genes, Genetica, 139:199-207 (2011). Looking just at nonsynonymous mutations, I count 37 mutations in guinea pigs and 44 in humans. Of these, a total of 3 are seen in both species. I’d say the evolutionary prediction – that different mutations would be seen in the two species – is fulfilled quite well, wouldn’t you?
If you agree that your argument about GULO was wrong, we can certainly move on to other arguments.
what is “actual test of evolution”? what evolution actually predict if it isnt true? (i mean not in this case but in general)
from what i know all the mutaions that appear in the rat sequence also appear in the mouse one. so if you will claim that its the result of mutations in the rat genome you need to deal with this, because in this way you can never know when is convergent and when it isnt (one way to find a convnergent is to find the same mutations in several genomes that are not close from phylogenetic prespective).
not realy. half of the human gulo is missing. it mean that the chance to get the same exon loss in other group is near 50% for any exon. so the chance to get the same 3 exon loss is very low. its mean that its not random at all.
now-you claim that evolution predict that the mutations will be different? its not true because we have a lot of cases of convergent. for example: the uox pseudogene share convergent mutations between gorila and orangutan. the prestin gene share 14 mutations between bat and a dolphin and so on.
A test of the prediction of evolutionary theory – the kind of test you said you were doing.
You didn’t answer the question: where are you getting this information from? In any case, it’s wrong.
7 out of 12 exons are missing. That means the chance of 3 missing guinea pig exons also being missing in humans is 20%, which is hardly low at all – it’s something that could easily happen by chance. In fact, it’s unlikely that they represent the same events, since one of the missing human exons is partially present in guinea pigs, suggesting two different mutations that deleted different portions of the gene.
You claimed that the mutations in humans and guinea pigs were the same. That’s wrong. Do you understand that or not? I don’t want to change to a new subject until we’re clear on this one.
In a word, no. You’ve looked at the data, picked one similarity, and then calculated the probability that that similarity would occur. That’s statistically meaningless. You’re also proposing something that has no biological mechanism, and you’re looking at the least informative part of the data. Why focus on the exons, when there are dozens of other mutations to compare? The great majority of those mutations follow the phylogenetic tree.
Also, you still haven’t answered the question: do you recognize that your original claim about shared mutations between guinea pigs and humans, taken from the GULO sequence paper, was wrong? Note what’s happened here: a creationist saw that paper, thought the shared mutations were a good argument against evolution and played them up. But if the paper misinterpreted them, suddenly they’re no longer evidence that has to be considered. That’s not how you do science – looking around for evidence that supports your premise and ignoring evidence that doesn’t.
No, we don’t agree on that. When did I say that hot spots were involved in exon loss? It’s possible, but I’ve seen no evidence for it in this case.
I think @Relates, Roger, should appreciate this quote from Patrick’s linked article!!!
"Senior author, Dr Anjali Goswami (UCL Genetics, Evolution & Environment), said: "When dinosaurs went extinct, a lot of competitors and predators of mammals disappeared, meaning that a great deal of the pressure limiting what mammals could do ecologically was removed."
" They clearly took advantage of that opportunity, as we can see by their rapid increases in body size and ecological diversity. Mammals evolved a greater variety of forms in the first few million years after the dinosaurs went extinct than in the previous 160 million years of mammal evolution under the rule of dinosaurs."
Of course I appreciate it. The problem is that we have known about this for a long time, and now the scientists are finally admitting that climate change brings about new species. This goes against the traditional Darwinian model that says that genetic change brings about new species.
What the study does not say although what it strongly implies and is true, is that climate changes caused by the asteroid strike and other factors closed down ecological niches favorable to the dinosaurs, causing them to die out, and opened ecological niches favorable to the plecental mammals causing them to flourish. This is how evolutionary change works, contrary to what Darwin thought and Dawkins thinks, and the way most evolutionary scientists think today.
Another study listed indicates that these changes in the environment began before the asteroid strike so that the position of the predatory dinosaurs was shaky before the strike which was the coup de grace. Again this puts environmental change in the forefront of evolutionary change contrary to scientific thought.
I can’t imagine a single evolutionary biologist finding anything at all surprising or controversial about the idea that climate change causes extinctions and opens new niches, and creates the possibility of new species. How many evolutionary biologists have you talked to about these issues?
Ecology is finally getting its due. And since nobody is falling on their sword about preserving Darwin’s ORIGINAL views … can we all move along onto the same page of the brand new book?
I think it is safe to say that today’s Evolutionary Scientists are perfectly happy with discussing issues of ecology.
Can you accept this? Or will you continue to post that somehow we are all being cheated by the scientists who hate to talk about ecology issues?
I’m no expert in evolutionary biology but I understand the philosophical implications involved. That climate change brings about new species does not go against the traditional Darwinian synthesis that genetic change brings about new species. Although this puts environmental change in the forefront of evolutionary change it is not contrary to scientific thought. If climate change brings about new species, it does not follow that genetic change does not bring about new species—the reason they are called new species is precisely because they have been genetically changed. Therefore, yes, climate change brings about new species for the simple reason that organisms become genetically changed. The semantics might be difficult for some to follow, however, it is clear and straightforward.
@Tony and @glipsnort, it is good to talk with you again.
Thank you for the positive feedback.
I am glad that we are in agreement. I really do not want to talk about my discussions with evolutionary biologists, but the meaning ecological evolution (to distinguish it from purely genetic evolution.)
The issue concerning evolution is not whether it occurs or not, but how it take place, and the issue here has been Is it guided or directed or not. Darwin as I understand him said that evolution was guided by Natural Selection. His understanding of how Natural Selection worked was based on Malthus’ population theories, which were succinctly described as “survival if the fittest.” However this view has never been verified and is not correct.
On the other hand the ecological view of species change has been scientifically verified and is correct. Ecological change takes place and this refers to many aspects in addition to climate change. Species within the environment are challenged to adapt to these changes.
Those who are able to do so will flourish and those who do not will not. It is that simple. No competition to survive, just adapting to the changes of nature.
It also reveals the purpose of evolution: to go and fill all the ecological niches of the earth with diversity of life, and eventually create humans in the Image of God, the Creator. The last point of course is an interpretation, but not far from the scientific evidence.
Survival of the fittest was always a useful phrase in terms of economy.
But perhaps it is helpful to actually break the phrase down into the “suite of concepts” it embodies:
Improved relative survival (individual better at avoiding getting eaten, and/or has greater life span);
Improved net fertility (individual has more offspring and/or has offspring that has more offspring and/or has offspring that is better at avoiding being eaten)
This can be because of ecological changes that newly favor one group of population members… or because of a new configuration of genetic factors in a group of population members.
You’re making distinctions that evolutionary biology doesn’t. All adaptive evolution represents adaptation to a particular environment, and that very much includes the ecological environment that is open to the organism. That has always been the understanding of evolutionary biologists, dating back to Darwin. At the same time, however, adaptive evolution always works by means of genetic changes filtered by natural selection. Those aren’t two views about how evolution proceeds: they’re two aspects of the same process. And yes, natural selection frequently involves competition between members of the same species.
Dawkins, who claims to speak for neoDarwinists and for the science of evolution in general (and I see very few people arguing against him,) claims that DNA is the sole engine of evolution. E. O. Wilson broke with him recently on the social nature of life that in particular points to the ability of social creatures, even insects, to adapt to new environments and this was supposed to be new.
Enough of the argument. Do you agree or disagree that ecological change directs evolution? If you disagree, give me an example.
You two are debating a single issue from two different directions.
Ecology makes different genes “winners” and “losers”.
Without the Genes … there would be no “winners” and “losers”.
Interestingly, if genes never changed, then changes in ecology wouldn’t be able to promote evolution. Conversely, however, ecology doesn’t ever have to change to have genetic changes (i.e., evolution) all by itself.
You’ve misunderstood them. As far as we know DNA(*) is the sole immediate cause of evolution. Every single evolutionary change takes place because of differences in DNA. Every one. But the changes that are selected for – that are responsible for adaptation – are almost always being driven by something in the environment. That doesn’t make them any less genetic. Ecology and DNA are both responsible for adaptive evolution.
(*) Leaving aside RNA viruses.
I wouldn’t use the word “directed”, since it suggests intentionality. But absolutely, adaptive evolution occurs in response to the environment, in directions made possible by the environment. Where have I suggested otherwise?
Now, can you give me an example of one of these changes that wasn’t mediated through changes to DNA?
I have tried to make it clear that I agree with Darwin in one important aspect. He divided evolution into two basic aspects, 1. (genetic) Variation and 2. Natural Selection.
Now as far as I am concerned, we are arguing about the nature of Natural Selection. I say that it is ecological. You seem to agree. I do not find anyone else who agrees with this position, certainly not Richard Dawkins, but that is besides the point.
“But absolutely, adaptive evolution occurs in response to the environment, in directions made possible by the environment.”