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Comparative biochemistry


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#1 dttom

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Posted 29 August 2007 - 10:23 AM

I am a student from hong kong who is preparing the biology syllubus in form six. overall speaking, the syllubus is easy while there are some points which for me as confusing as I believe the evidence and information provided by the book is not convincible enough; I have tried asking my teacher while he said this is what the marking scheme limits and could not be changed and the issue is controversial and could not give me any relatively absolute answer.

The issue I am concerning is about comparative biochemistry used in the study of evolution. For instance, consider the haemoglobin protein in chimpanzee and in human, which differ in only one amino acid. It is then assume that the chimpanzee is the closest relative of human compared with other primates which differ with haemoglobin protein sequence in human by more than one amino acid. For this expanation, which I think is not convincible, I don't think there are two points worth further consideration, which would be discuss below.

For haemoglobin in human and that in chimp differs in one amino acid, whether it implies similarity in DNA is worth discussion, I think. First of all, it is generally known that protein is transcribed and then translated from DNA, as in case of haemoglobin here; however, similarity in amino acid sequence in protein does not imply similarity in DNA, as what DNA expresses is region called exons, while DNA contains also so-called introns, which in amount is greater than exons by few folds, hence similarity in protein only imply similarity in DNA exons but not include introns. If there are mutations act on introns regions of DNA, their effect would not be expressed in the protein translated and hence would be misunderstood as not ever occurred. Consider such an extreme hypothetical circumstance, which its extremity is only of easy understanding, that there is an ancestral species, A; with three derivative species, A', A" and A"'. Imagine that if A' is formed by relatively fewer mutation act on exons but large number of such act on introns regions, and that it is the variation which differ from the mainstream species A; A" derive from A by mutations acting almost utterly on exons; and A"' from A by having minimal amount of mutation hence could be considered as living fossil of A. Now if we compare certain proteins, those which those mutations act on in this case, for easier understanding, it would be found that protein from A" is more similar to that in A"' than when comparing the same protein from A' to A"'. While from the reasonable assumption that A' derived from A was prior to derivation of A" from A, we could say that such conclusion from so-called comparative biochemistry is opposing that assumption. So now only holding this point, it could be observed that the assumption that, the more similar two proteins are, more closely the two possessers are in phylogenetic relationship, is in this aspect not with enough evidence supporting.

Another concern the rate of mutation, apart from matter of introns and exons, rate of muation does matter. For a simple phylogenetic tree that A to A', B and C that C derived from A prior to derivation of B from A, ancestral A forms A' with minimal muation and change. When C derived from A, if C got into a place where mutation seldom occurred or occurred at a slower rate; and that when B derived from A, B got into a place full of ultraviolet radiation or cosmic ray which both increase the mutation rate; mutation accumulated by B would possibly much more than that by C and if we compare their DNA sequences with the living fossil A', we would probably find that C differs from A' in a degree smaller than the case of comparing B to A'. For this circumstance, we if use the current logic to obstain results, we may get into an incorrect result that C is more related to A' than B, which from my example that this is not the correct conclusion. From this consideration, we again could find that the current method of getting phylogenetic relatedness between species is not reliable enough.

The above of course is only my point of view, not knowing its reliability, so here I would like to gather more opinion from more people and any one who could give comments would be helpful.
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#2 foodchain

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Posted 30 August 2007 - 01:18 AM

I am a student from hong kong who is preparing the biology syllubus in form six. overall speaking, the syllubus is easy while there are some points which for me as confusing as I believe the evidence and information provided by the book is not convincible enough; I have tried asking my teacher while he said this is what the marking scheme limits and could not be changed and the issue is controversial and could not give me any relatively absolute answer.

The issue I am concerning is about comparative biochemistry used in the study of evolution. For instance, consider the haemoglobin protein in chimpanzee and in human, which differ in only one amino acid. It is then assume that the chimpanzee is the closest relative of human compared with other primates which differ with haemoglobin protein sequence in human by more than one amino acid. For this expanation, which I think is not convincible, I don't think there are two points worth further consideration, which would be discuss below.

For haemoglobin in human and that in chimp differs in one amino acid, whether it implies similarity in DNA is worth discussion, I think. First of all, it is generally known that protein is transcribed and then translated from DNA, as in case of haemoglobin here; however, similarity in amino acid sequence in protein does not imply similarity in DNA, as what DNA expresses is region called exons, while DNA contains also so-called introns, which in amount is greater than exons by few folds, hence similarity in protein only imply similarity in DNA exons but not include introns. If there are mutations act on introns regions of DNA, their effect would not be expressed in the protein translated and hence would be misunderstood as not ever occurred. Consider such an extreme hypothetical circumstance, which its extremity is only of easy understanding, that there is an ancestral species, A; with three derivative species, A', A" and A"'. Imagine that if A' is formed by relatively fewer mutation act on exons but large number of such act on introns regions, and that it is the variation which differ from the mainstream species A; A" derive from A by mutations acting almost utterly on exons; and A"' from A by having minimal amount of mutation hence could be considered as living fossil of A. Now if we compare certain proteins, those which those mutations act on in this case, for easier understanding, it would be found that protein from A" is more similar to that in A"' than when comparing the same protein from A' to A"'. While from the reasonable assumption that A' derived from A was prior to derivation of A" from A, we could say that such conclusion from so-called comparative biochemistry is opposing that assumption. So now only holding this point, it could be observed that the assumption that, the more similar two proteins are, more closely the two possessers are in phylogenetic relationship, is in this aspect not with enough evidence supporting.

Another concern the rate of mutation, apart from matter of introns and exons, rate of muation does matter. For a simple phylogenetic tree that A to A', B and C that C derived from A prior to derivation of B from A, ancestral A forms A' with minimal muation and change. When C derived from A, if C got into a place where mutation seldom occurred or occurred at a slower rate; and that when B derived from A, B got into a place full of ultraviolet radiation or cosmic ray which both increase the mutation rate; mutation accumulated by B would possibly much more than that by C and if we compare their DNA sequences with the living fossil A', we would probably find that C differs from A' in a degree smaller than the case of comparing B to A'. For this circumstance, we if use the current logic to obstain results, we may get into an incorrect result that C is more related to A' than B, which from my example that this is not the correct conclusion. From this consideration, we again could find that the current method of getting phylogenetic relatedness between species is not reliable enough.

The above of course is only my point of view, not knowing its reliability, so here I would like to gather more opinion from more people and any one who could give comments would be helpful.


I donít know exactly what you are asking here. Comparative physiology exists because you can do it, its rather simple. Its not like someone said hey, the circle is a shape like a square so one must have evolved from the other. Similarities in organisms goes far beyond even the example you posed, and another aspect that you may not grasp enough or do is simply evolution. Things are going to change. Comparing a human to a microbe, then to a mouse, then to a chimp makes evolution more evident. Its also something that can be verified in a laboratory for a diverse amount of situations, such as even telling if known where a person might have gotten a disease from in regards to another person that was a carrier. If evolution did not exist, science would not be able to piece it together, its a rather black and white point about reality, as demonstrated in natural history, and in scientific experiments a lay person can come to learn how to do all on their own. Such as if you keep a generation of microbes, and follow if you will change in them over time. For instance, a more easy to notice aspect of this is somewhere back in our lineage evolutionary speaking the ability to internally manufacture ascorbic acid, the genes responsible for such basically mutated, this mutation has passed along via evolution into modern human genetic code, its but one example of basically a very large pool of such examples of concrete, very specific and hard physical evidence. I donít think it also leads to much of the ability to get philosophical with such in the sense of evidence. Now if you want to trail off on that, the point about biology and why its still able to function as a diverse amount of scientific fields with evolution being the backbone of such a science is that constant scientific efforts everyday by a rather large amount of professionals from say medical science to zoology use such to understand life successfully. Is it 100% understood, no, but what does that say, and what really is? Gravity is not 100% understood, it does not stop such from being physically real, and or understandable.
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#3 dttom

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Posted 30 August 2007 - 04:06 AM

I don’t know exactly what you are asking here. Comparative physiology exists because you can do it, its rather simple. Its not like someone said hey, the circle is a shape like a square so one must have evolved from the other. Similarities in organisms goes far beyond even the example you posed, and another aspect that you may not grasp enough or do is simply evolution. Things are going to change. Comparing a human to a microbe, then to a mouse, then to a chimp makes evolution more evident. Its also something that can be verified in a laboratory for a diverse amount of situations, such as even telling if known where a person might have gotten a disease from in regards to another person that was a carrier. If evolution did not exist, science would not be able to piece it together, its a rather black and white point about reality, as demonstrated in natural history, and in scientific experiments a lay person can come to learn how to do all on their own. Such as if you keep a generation of microbes, and follow if you will change in them over time. For instance, a more easy to notice aspect of this is somewhere back in our lineage evolutionary speaking the ability to internally manufacture ascorbic acid, the genes responsible for such basically mutated, this mutation has passed along via evolution into modern human genetic code, its but one example of basically a very large pool of such examples of concrete, very specific and hard physical evidence. I don’t think it also leads to much of the ability to get philosophical with such in the sense of evidence. Now if you want to trail off on that, the point about biology and why its still able to function as a diverse amount of scientific fields with evolution being the backbone of such a science is that constant scientific efforts everyday by a rather large amount of professionals from say medical science to zoology use such to understand life successfully. Is it 100% understood, no, but what does that say, and what really is? Gravity is not 100% understood, it does not stop such from being physically real, and or understandable.


I know that organism would change with time, with the effect of mutation and natural selection and lastly may be even speciation, resulting in both micro- and macro- evolution. while what I am asking is about the method of carrying out comparative biochemistry; from my text book it is said that it could be done by comparing amino acid sequence of homologus protein, here haemoglobin, from two different species, after obtaining the result between these two species; any one from these two is again compared with the third species and result is obtained and recorded; then compare the records, relatedness could be obtained by noting the amino acid sequence difference (no. of amino acid differed). Here I think there is a problem of inaccuracy as mentioned in the above passage...
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