yep, but you realy think that its work in the same efficiency? i doubt it.
actually we get many different result by checking different genes. see here for instance:
https://www.nature.com/news/phylogeny-rewriting-evolution-1.10885
we cant know it for sure. its seens logical that a fish insulin for instance will have a gene that is more similar to other fishes since they may share similar diet, environment etc.
Do you have any interest in testing this hypothesis? If this hypothesis were true, we should see correlations between diet and insulin sequence. If this is not true, you would need to drop it as an explanation and find another specific factor (not merely âenvironmentâ).
scd: yep, but you realy think that its work in the same efficiency? i doubt it.
It doesnât matter what I think, thatâs just what the evidence shows: âHumanâ insulin versus animal insulin in people with diabetesmellitus
Background:
Human insulin was introduced for the routine treatment of diabetes mellitus in the early 1980s without adequate comparison of efficacy to animal insulin preparations. First reports of altered hypoglycaemia awareness after transfer to human insulin made physicians and especially patients uncertain about potential adverse effects of human insulin.Objectives:
To assess the effects of different insulin species by evaluating their efficacy(in particular glycaemic control) and adverse effects profile (mainly hypoglycaemia).Search strategy:
A highly sensitive search for randomised controlled trials combined with key terms for identifying studies on human versus animal insulin was performed using The Cochrane Library , MEDLINE and EMBASE. We also searched reference lists and databases of ongoing trials.Selection criteria:
We included randomised controlled clinical trials with diabetic patients of all ages that compared human to animal (for the most part purified porcine) insulin. Trial duration had to be at least one month in order to achieve reliable results on the main outcome parameter glycated haemoglobin.Data collection and analysis:
Trial selection as well as evaluation of study quality was performed by two independent reviewers. The quality of reporting of each trial was assessed according to a modification of the quality criteria as specified by Schulz and by Jadad.Main results:
Altogether 2156 participants took part in the 45 randomised controlled studies that were discovered through extensive search efforts. Though many studies had a randomised, double-blind design, most studies were of poor methodological quality. Purified porcine and semi-synthetic insulin were most often investigated. No significant differences in metabolic control or hypoglycaemic episodes between various insulin species could be elucidated. Insulin dose and insulin antibodies did not show relevant dissimilarities.
scd: actually we get many different result by checking different genes. see here for instance:
Let me explain why this doesnât mean what you think it means. Phylogenetic trees are like measurements, they donât have to match exactly to still be significantly similar. And so similar in degree the only good explanation is that they are that similar because they underwent the shame genealogical history.
To see what I mean, Imagine I give you two ultra-sensitive thermometers to measure the temperature in my living room to test the hypothesis that thereâs a relatively uniform temperature everywhere in the room. And they agree to the 6âth decimal place, where they disagree. They each measure 20.0330413 and 20.0330415 degrees C. Does this cast a significant doubt on the uniform temperature of the room?
Or I give you two thousand normal thermometers and place them all over the room, and most of them measure 20 or 21 degrees, and once in every 100 thermometers, thereâs on that says 26, and one that says 17. Does that cast doubt on the hypothesis? We have to answer such questions using statistics.
The disagreement between phylogenetic trees is not of such a magnitude that they cause doubt on the general conclusion that species share common ancestry. They are still incredibly similar.
From Douglas Theobaldâs 29+ Evidences for macroevolution article we find Prediction 1.3: Consilience of independent phylogenies
When two independently determined trees mismatch by some branches, they are called âincongruentâ. In general, phylogenetic trees may be very incongruent and still match with an extremely high degree of statistical significance (Hendy et al. 1984; Penny et al. 1982; Penny and Hendy 1986; Steel and Penny 1993). Even for a phylogeny with a small number of organisms, the total number of possible trees is extremely large. For example, there are about a thousand different possible phylogenies for only six organisms; for nine organisms, there are millions of possible phylogenies; for 12 organisms, there are nearly 14 trillion different possible phylogenies (Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). Thus, the probability of finding two similar trees by chance via two independent methods is extremely small in most cases. In fact, two different trees of 16 organisms that mismatch by as many as 10 branches still match with high statistical significance (Hendy et al. 1984, Table 4; Steel and Penny 1993). For more information on the statistical significance of trees that do not match exactly, see âStatistics of Incongruent Phylogenetic Treesâ.
The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:
âBiologists seem to seek the âThe One Treeâ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.â (Penny and Hendy 1986, p. 414)
scd: we cant know it for sure. its seens logical that a fish insulin for instance will have a gene that is more similar to other fishes since they may share similar diet, environment etc.
First of all I think âknowing for sureâ is a red herring. We donât know anything âfor sureâ.
But it doesnât matter what you think sounds logical, what matters is what the molecular biology of living organisms is really like, and it isnât what your intuitions tell you is âlogicalâ. The whole point of my post was to show you that your intutions here are wrong.
Of course, humans can significantly alter their diets, and their insulin gene sequence doesnât change. It is possible to live on high protein, or high fat, or high carbohydrate diets, and it doesnât change the insulin gene sequence. It affects your metabolism, and how your body responds to insulin (some diets can lead to diabetes of course), but it doesnât change the sequence of the gene.
its just one possible explanation out of many. so im not sure about that.
That doesnât appear to have held up over the last 6 years. Why would you cite something from the gossip section and not an actual scientific paper?
If youâre looking for truth, do you quit after finding one thing you can use as ammunition, or do you keep looking?
Micro-RNAs turn out to be problematic as analyzed by Peterson. See Thomson, R. C., Plachetzki, D. C., Mahler, D. L. & Moore, B. R. A critical appraisal of the use of microRNA data in phylogenetics. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1407207111 (2014)
Youâre confused. The question is not whether some of the differences between similar genes found in different species have particular physiological effects that affect their function, and therefore affect how they interact with other genes in the species. Some of those differences are there because they do have a functional consequence of some sort, this is not in dispute.
The question we are considering is whether the types of mutations in similar genes shared between different species, that have functional consequences, should be expected to constrain independently inferred phylogenetic trees to converge on a similar topology.
Before we proceed on this question, do you understand this distinction?
not according to this article:
Phylogeny: Rewriting evolution | Natureyou can see that these are completely different trees and no similar at all.
Thatâs actually not correct. In both trees, cow and dog are more closely related to each other than to everything else. In both trees, both rat and mouse are more closely related to each other than to everything else. The main differences seem to be which clades nest into which. Little to nothing can be concluded on the basis of what appears to me just a drawing made for emphasis.
Second, even supposing those two are real phylogenetic trees inferred from data, the significance of the incongruence has not been worked out anywhere that I can see, and the question is how that would change with a larger taxon sample or more loci included in both data sets. It also isnât clear what methodology, or data sources, were even used to infer those trees.
I looked up Kevin Petersonâs google scholar page, and since that pop-sci article has been written, Kevin Peterson and colleagues have proceeded to publish an actual mammalian tree based on a superalignment of 16,050 pre-miRNA genes, and compared it to a tree inferred from protein coding genes. This is their result:
These trees look almost completely congruent to me. As far as I can see there are only three mismatching branches, and thatâs because some branch from each tree is missing which is present in the other.
I wouldnât call that a mismatch, just missing data. There is one actual mismatch: the position of the tree shrew
Youâre right, didnât even see that one before now.
You donât seem to understand the difference between these two questions:
A) What is the true interrelationship between living species?
B) Do they even share common descent?
The papers you are digging up here are all attempts to answer question A. The magnitude of the differences between these phylogenetic trees are not significantly incongruent. They are incongruent enough that it makes the placements of certain nodes relative to each other within the tree subject to uncertainty, but they are not so incongruent that they cast doubt on the existence of the tree.
Do you understand this distinction?
This was addressed already in the first article I linked you from Douglas Theobaldâs 29+ Evidences for macroevolution: Prediction 1.3: Consilience of independent phylogenies
In science, independent measurements of theoretical values are never exact. When inferring any value (such as a physical constant like the charge of the electron, the mass of the proton, or the speed of light) some error always exists in the measurement, and all independent measurements are incongruent to some extent. Of course, the true value of something is never known for certain in scienceâall we have are measurements that we hope approximate the true value. Scientifically, then, the important relevant questions are âWhen comparing two measurements, how much of a discrepancy does it take to be a problem?â and âHow close must the measurements be in order to give a strong confirmation?â Scientists answer these questions quantitatively with probability and statistics (Box 1978; Fisher 1990; Wadsworth 1997). To be scientifically rigorous we require statistical significance. Some measurements of a given value match with statistical significance (good), and some do not (bad), even though no measurements match exactly (reality).
(âŚ)
The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al . 2002; Penny et al . 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:
âBiologists seem to seek the âThe One Treeâ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al . 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.â (Penny and Hendy 1986, p. 414)
i think that we already discussed this. again: i think that its logical to conclude that a reptile insulin should be more silimar to other reptiles insulin then to say a mammal one. also remember again that many genes produce different trees:
see the paper above. more gene will not necessarily solve the problem. but even if it was true, so what? as we have seen we can make a tree of vehicles:
but again: it doesnt prove any evolution.
We are not talking about why the genes are merely similar. We are talking about why they are similar in such a way that a phylogenetic algorithm would infer highly similar trees from independent sets of data.
So you clearly didnât understand this. We are trying to determine why it is that different sources of comparative biological data (morphology, gene or protein sequences) consistently produces trees with a statistically significant degree of congruence. This is not actually explained by the statement âI think its logical to cnclude that a reptile insulin should be more similar to other reptile insulins then to say a mammal oneâ.
Second, merely listing trees that have incongruences does not suffice to cast any doubt on the existence of a common topology for reasons already explained previously.
Third, your ability to make a cartoon tree and place objects haphazardly at the leaves has absolutely nothing to do with how phylogenetic trees are actually made and does not contitute evidence that you can consistently find that shared characteristics of designed objects can be objectively sorted into a nesting hierarchical arrangement, and that different characteristics significantly agree on a common topology. Do you even understand what I just wrote means?
its basically the same. a tipical mammal is more similar to a mammal then to a reptile. so a mammal insulin should group with other mammal insulin. now, we can conclude the same for intergroup species. for insance: a chimp insulin should be more similar to a gorila insulin then to say a dolphin one (although they are all mammals). in this way we eventually will end up with a tree.
actually they are both made by difference-similarity comparison. say that we are talking now about phylogeny base on morphology. now, do you agree for instance that an airplane is more similar to other airplane then to a car and therefore will group with other airplane? if so its the same like in animal phylogeny.
No, it is NOT the same. Thatâs the whole point here. There are patterns in the similarity. Tree patterns. And the tree patterns keep correlating to an extremely high degree of statistical significance. Why?
a tipical mammal is more similar to a mammal then to a reptile. so a mammal insulin should group with other mammal insulin
Why?
now, we can conclude the same for intergroup species. for insance: a chimp insulin should be more similar to a gorila insulin then to say a dolphin one
Why should that be the case?
(although they are all mammals). in this way we eventually will end up with a tree.
Yes, and why should that be the case?
actually they are both made by difference-similarity comparison.
What is that? Never heard of it. Try to explain what that is.
say that we are talking now about phylogeny base on morphology. now, do you agree for instance that an airplane is more similar to other airplane then to a car and therefore will group with other airplane?
I would certainly agree that airplanes have similarities that make them recognizable as airplanes. I donât agree that you can objectively sort airplanes into nesting hiearchies from shared derived characteristics. And I certainly donât agree that you can pick different, independent shared attributes of airplanes and derive statistically signicantly congruent phylogenetic trees from them.
if so its the same like in animal phylogeny.
That claim has not met itâs burden of proof, and at this stage I doubt you know how to even begin to address that.
That is not how phylogenetic trees are made. You didnât know?
It was in the news section. Do you not know the difference?
Thatâs not similar because itâs much further back in time, where we expect more fuzziness. I note that you didnât answer my question, so I must conclude that you have no interest in finding the truth, just in arguing. Is that accurate?
because of their morphology. if their morphology is similar then why we should not expect to find that their genes will be similar too? it make sense that if 2 creatures are more similar to each other then to any other creatures we should find that their genes are more similar too. again; it make sense that a chimp insulin will be more similar to human insulin then to a dolphin one. do you agree?
a phylogenetic tree is basically a tree of similarity comparison. the same is true for my vehicles comparison.
show me why not. whats wrong with this tree for instance?:
Micro-RNAs turn out to be problematic as analyzed by Peterson
