DNA Do we really know all about it?

Posted:
in General Discussion edited January 2014
With DNA I believe far too often claims are made without the due intel being found. In other words many in the field make claims based on tid bits of info vs/ waiting it out and really understanding the science before lumping out statements.



For example: Who has not heard that human DNA is 98% identical to chimpanzee DNA? We have heard such claims for years now.



I must ask what is such a stat based on? ? ?



tid bits which conclude an end or a fully composite view of the entire science?



Consider the following:



Jonathan Marks, (department of anthropology, University of California, Berkeley) has pointed out the often-overlooked problem with this "similarity" line of thinking.



Because DNA is a linear array of those four bases A,G,C, and T only four possibilities exist at any specific point in a DNA sequence. The laws of chance tell us that two random sequences from species that have no ancestry in common will match at about one in every four sites. Thus even two unrelated DNA sequences will be 25 percent identical, not 0 percent identical.



Therefore a human and any earthly DNA-based life form must be at least 25% identical. Would it be correct, then, to state that daffodils are one-quarter human?? The idea that a flower is one-quarter human is neither profound nor enlightening; it is outlandishly ridiculous!



One of the downfalls of previous molecular genetic studies has been the limit at which chimpanzees and humans could be compared accurately. Scientists often would use only 30 or 40 known proteins or nucleic acid sequences, and then from those extrapolate their results for the entire genome. Today, however, we have the majority of the human genome sequences, practically all of which have been released and made public. This allows scientists to compare every single nucleotide base pair between humans and primates something that was not possible prior to the human genome project. In January 2002, a study was published in which scientists had constructed and analyzed a first-generation human chimpanzee comparative genomic map. This study compared the alignments of 77,461 chimpanzee bacterial artificial chromosome (BAC) end sequences to human genomic sequences. Fujiyama and colleagues detected candidate positions, including two clusters on human chromosome 21, that suggest large, nonrandom regions of differences between the two genomes. In other words, the comparison revealed some large differences between the genomes of chimps and humans.



Amazingly, the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] This study compared the alignments of 77,461 chimpanzee sequences to human genomic sequences obtained from public databases. Of these, 36,940 end sequences were unable to be mapped to the human genome. Almost 15,000 of those sequences that did not match human sequences were speculated to correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons?



Speaking of the human Y chromosome check out the following:



Y chromosome



All I would suggest is that those in genetic fields practice due study and consideration before lumping out stats to the general public.



I am not against science in any way I just advocate honesty in reporting.



What are your thoughts about stats lumped at the public regarding genetics? Do you find them accurate? Do you find yourself asking more questions?



Fellowship
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Comments

  • Reply 1 of 56
    billybobskybillybobsky Posts: 1,914member
    Fellows,

    But the genes in your body are not random. That is what they are looking at when they say 98% similarity, the actual sequence of the known functional DNA for known functional gene products (ie proteins). If we looked at some non-coding region, the analysis of stat would work, but without consideration of the biases towards functional versus non-functional proteins it is somewhat silly to even argue along that line. For quite a few genes, humans share a greater than 70% identity with fellow mammals. Ah, this is where I agree that using actual genes is irrevocably complicated in trying to sort out relationships -- they are good indicators but they dont have as broad of an array of options because they are not completely random -- you can see gradual changes amongst a group of presumably related species and greater changes between presumable unrelated species, but between closely related species its very hard to determine an actual system of assignment. Most people constructing relationship maps (or evolutionary trees of living cellular organisms) use more or less random portions of the sRNA of ribosomes to set up relationships between species. These portions are random so the minimum relationship is (if the berkeley guy did his number cruching correctly) 25% and the maximum relationship is 100%. Anything greater than say 30% is significant, lets say...
  • Reply 2 of 56
    fellowshipfellowship Posts: 5,038member
    Quote:

    Originally posted by billybobsky

    Fellows,

    But the genes in your body are not random. That is what they are looking at when they say 98% similarity, the actual sequence of the known functional DNA for known functional gene products (ie proteins). If we looked at some non-coding region, the analysis of stat would work, but without consideration of the biases towards functional versus non-functional proteins it is somewhat silly to even argue along that line. For quite a few genes, humans share a greater than 70% identity with fellow mammals. Ah, this is where I agree that using actual genes is irrevocably complicated in trying to sort out relationships -- they are good indicators but they dont have as broad of an array of options because they are not completely random -- you can see gradual changes amongst a group of presumably related species and greater changes between presumable unrelated species, but between closely related species its very hard to determine an actual system of assignment. Most people constructing relationship maps (or evolutionary trees of living cellular organisms) use more or less random portions of the sRNA of ribosomes to set up relationships between species. These portions are random so the minimum relationship is (if the berkeley guy did his number cruching correctly) 25% and the maximum relationship is 100%. Anything greater than say 30% is significant, lets say...




    The trouble is looking over the so-called "Junk" DNA.

    A recent study has shown that genes (as many as five at a time) are found within the introns of other genes. This kind of arrangement results in the simultaneous expression of all of these genes during transcription of the gene in question. Such regulatory control is rather remarkable, suggesting intelligent designed as opposed to random chance. Some of the non-coding DNA is loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. Tandemly repeated sequences frequently considered as functionless "junk" are found to be grouped into certain classes of repeat unit lengths, indicating functional involvement of these sequences. It is likely these tandem repeats play the role of weak enhancer-silencers that modulate, in a copy number-dependent way, the expression of proximal genes.



    Well over 700 studies (over 100 in the last year) have demonstrated the role of non-coding DNA as enhancers for transcription of proximal genes. These intronic enhancers have been described for eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), the variable region of the rearranged immunoglobulin mu (IgM) gene, the alpha-globin gene, the activin beta A subunit gene, lambda 2 light chain transgenes, Human CYP1B1, a member of the cytochrome P450 superfamily, immunoglobulin heavy chain (IgH), alcohol dehydrogenase, 3 alpha-hydroxysteroid dehydrogenases, apolipoprotein A-II, beta1,4-N-acetylgalactosaminyltransferase, kappa light chain gene, Alpha-1 acid glycoprotein, the T-cell receptor beta-chain, 2-crystallin, 1 tubulin gene, aldolase B gene, and many others.



    Another 60+ studies have demonstrated the role of non-coding DNA as silencers for suppression of transcription of proximal genes. The presence of silencer genes has been shown to down-regulate the apolipoprotein A-II gene, the osteocalcin gene, the 2-crystallin gene, the CD4 gene, the beta globin gene, the gene for the neuron-glia cell adhesion molecule, Ng-CAM, the renin gene, the keratin 18 gene, the platelet-derived growth factor A-chain gene , and dozens of other genes.



    There is more to the picture



    Fellowship
  • Reply 3 of 56
    Quote:

    Originally posted by FellowshipChurch iBook





    Therefore a human and any earthly DNA-based life form must be at least 25% identical. Would it be correct, then, to state that daffodils are one-quarter human?? The idea that a flower is one-quarter human is neither profound nor enlightening; it is outlandishly ridiculous!




    Fellows, you misunderstand the science a bit here methinks. DNA is a set of instructions that makes 'sentences' with a four-letter vocabulary but there are an unimagineably huge amount of these 'sentences'. 'Hamlet' was written with the same 26 letters used to write every thread in 'Temporary Insanity' but the only thing they have in common is the alphabet, after all: they're not really very similar at all.
  • Reply 4 of 56
    fellowshipfellowship Posts: 5,038member
    Quote:

    Originally posted by Hassan i Sabbah

    Fellows, you misunderstand the science a bit here methinks. DNA is a set of instructions that makes 'sentences' with a four-letter vocabulary but there are an unimagineably huge amount of these 'sentences'. 'Hamlet' was written with the same 26 letters used to write every thread in 'Temporary Insanity' but the only thing they have in common is the alphabet, after all: they're not really very similar at all.



    You make my point for me very well indeed Hassan



    Thanks
  • Reply 5 of 56
    matsumatsu Posts: 6,558member




    I wish you'd just get a clue.
  • Reply 6 of 56
    709709 Posts: 2,016member
    You've been asking a lot of strange (for you) questions lately Fellows...did you meet a cute Creationist girl or something?
  • Reply 7 of 56
    andersanders Posts: 6,523member
    Quote:

    Originally posted by 709

    You've been asking a lot of strange (for you) questions lately Fellows...did you meet a cute Creationist girl or something?



    Huh? You must be mistaken. I have notised a few NON-strange posts from FSiB lately. This is the standart goods.



    Have you met a cute democrat girl lately fellowship?



    Still like you. How can you not like someone who invite you over for doughnuts?
  • Reply 8 of 56
    709709 Posts: 2,016member
    Maybe the whole Age Of The Universe / Crop Circle / and something about him wanting a Harem threw me off.
  • Reply 9 of 56
    billybobskybillybobsky Posts: 1,914member
    Quote:

    Originally posted by FellowshipChurch iBook

    The trouble is looking over the so-called "Junk" DNA.

    A recent study has shown that genes (as many as five at a time) are found within the introns of other genes. This kind of arrangement results in the simultaneous expression of all of these genes during transcription of the gene in question. Such regulatory control is rather remarkable, suggesting intelligent designed as opposed to random chance. Some of the non-coding DNA is loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. Tandemly repeated sequences frequently considered as functionless "junk" are found to be grouped into certain classes of repeat unit lengths, indicating functional involvement of these sequences. It is likely these tandem repeats play the role of weak enhancer-silencers that modulate, in a copy number-dependent way, the expression of proximal genes.



    Well over 700 studies (over 100 in the last year) have demonstrated the role of non-coding DNA as enhancers for transcription of proximal genes. These intronic enhancers have been described for eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP), the variable region of the rearranged immunoglobulin mu (IgM) gene, the alpha-globin gene, the activin beta A subunit gene, lambda 2 light chain transgenes, Human CYP1B1, a member of the cytochrome P450 superfamily, immunoglobulin heavy chain (IgH), alcohol dehydrogenase, 3 alpha-hydroxysteroid dehydrogenases, apolipoprotein A-II, beta1,4-N-acetylgalactosaminyltransferase, kappa light chain gene, Alpha-1 acid glycoprotein, the T-cell receptor beta-chain, 2-crystallin, 1 tubulin gene, aldolase B gene, and many others.



    Another 60+ studies have demonstrated the role of non-coding DNA as silencers for suppression of transcription of proximal genes. The presence of silencer genes has been shown to down-regulate the apolipoprotein A-II gene, the osteocalcin gene, the 2-crystallin gene, the CD4 gene, the beta globin gene, the gene for the neuron-glia cell adhesion molecule, Ng-CAM, the renin gene, the keratin 18 gene, the platelet-derived growth factor A-chain gene , and dozens of other genes.



    There is more to the picture



    Fellowship




    Fellows,

    Again, I dont think you can leap to suggest intelligent design, its irrational to do so (actually quite irrational). Regardless, I am not going to argue the subtleties of gene regulation with you, there are far more intriguing systems than those cited. I think you need to learn the science behind the words you wrote (or copied) before you follow the leaps they make...
  • Reply 10 of 56
    brbr Posts: 8,395member
    Move along nothing to see here.



  • Reply 11 of 56
    toweltowel Posts: 1,479member
    Fellowship, I think if you asked a biologist whether "junk DNA" has any functional significance, he's give respond with a more eloquent version of "duh". The first report of a tRNA gene within an intron was in 1981. Since then we've found many, many more intron-encoded tRNAs, and entire new classes of nontranslated RNAs within introns (snoRNAs, siRNSA, miRNAs, etc). The existence of enhancers and represssors, both within promoters (very close to coding regions) and elsewhere have been known for literally decades. It's also known that most introns and most of the intergenic space is, indeed, junk. I think part of the problem is that the public perception of science lags the actual science by many years. And that the public perception of science is generally an over-simplisitic one.



    It's perfectly valid to say, based on comparisons of only coding regions, that humans and chimps are 98% identical. Because most of what isn't in the coding regions is junk. Or at least non-selected, replaceable "filler". It's at least as valid to say that we're 48% identical, based on comparisons of the entire genome. Remember that humans and chips diverged millions of years ago and that the vast majority of the genome is not under selection (you're ok with "microevolution", right?). Even 48% identity in those cirumstances is hugely, unimaginably significant. A quick exercise in probably tell us that if each genome was only 300bp long, and the probability of having a match at random was 25%, the probability of 150 (about 50%) of those 300bp matching is 1x10-20. Decimal place, nineteen zeros, one. That's pretty significant. And the genomes are actually 3 billion bp long, not 300. Unfortunately, I'd have to book time on a supercomputer to compute the real probability, but it would probably be about the smallest number ever calculated.



    What's bothering you, probably, is this idea of being X% like a chimp. The public, or at least the media, creates the false impression that that's what the scientists mean. Who could put a % on how much we're like chimps? What we can say is that we share quite a bit of DNA with them, that we're almost identical in regions we think are functionally significant, and we are certainly more like them than any other species.
  • Reply 12 of 56
    billybobskybillybobsky Posts: 1,914member
    in honor of Hasan, yay for the above post.
  • Reply 13 of 56
    brussellbrussell Posts: 9,812member
    This thread reminded me of this story I saw a few weeks ago: Study: Chimps Belong In Human Genus

    Basically, they're saying that chimps are human. Or maybe, that humans are chimps.



    Quote:

    According to Morris Goodman, one of the paper's authors and a professor of anatomy at Wayne State University School of Medicine, and his colleagues, the DNA information, combined with the ancestral links, should result in a new family tree, with the genus Homo including humans, common chimpanzees, and bonobo chimpanzees. Chimps are currently classified in the genus Pan. "Chimps are more like a human than a gorilla," said Goodman.



    Quote:

    "Richard Dawkins perhaps provided the best visual for our link to chimps," Fouts told Discovery News. "Imagine taking the hand of your grandmother, who was holding the hand of her grandmother and so on down the line. 155 miles out, one of the women would be holding the hand of a chimpanzee."





    Don't have a stroke when you read it, Fellowship. We need you around here.
  • Reply 14 of 56
    fellowshipfellowship Posts: 5,038member
    Quote:

    Originally posted by BRussell

    This thread reminded me of this story I saw a few weeks ago: Study: Chimps Belong In Human Genus

    Basically, they're saying that chimps are human. Or maybe, that humans are chimps.







    Don't have a stroke when you read it, Fellowship. We need you around here.




    I read that as well. I am just a guy that posts here on AI. That guy gets a lot of press and wants to change the record all the sudden. One has to wonder where we temper ourselves with science. I am all for science as I have said over and over my only area of questioning is over what is reported. Quite frankly a large bit is reported. What is indeed fact could be another matter in many cases. I just like to ask questions and bounce them off you all. If I am off base over something I am humbled by getting feedback from the members.



    Of course I find this interesting: Robert May is a UK Chief Scientist. In New Scientist magazine (July 1, 2000) on page 5 he stated, We share half our genes with the banana. One can only guess (with a fertile imagination) what the common ancestor between people and bananas looked like! In addition, there are fish that have 40% the same DNA as people, but hopefully no evolutionist would claim that the fish are 40% human or people are half bananas.



    half bananas!! I am starting to think some people are half bananas!



    Don't look at me that way I mean come on look at the DNA!!!



    snoitseuq ksa



    Fellowship
  • Reply 15 of 56
    fellowshipfellowship Posts: 5,038member
    double sorry
  • Reply 16 of 56
    xenuxenu Posts: 204member
    Quote:

    Originally posted by FellowshipChurch iBook



    Of course I find this interesting: Robert May is a UK Chief Scientist. In New Scientist magazine (July 1, 2000) on page 5 he stated, We share half our genes with the banana. One can only guess (with a fertile imagination) what the common ancestor between people and bananas looked like! In addition, there are fish that have 40% the same DNA as people, but hopefully no evolutionist would claim that the fish are 40% human or people are half bananas.



    half bananas!! I am starting to think some people are half bananas!



    Don't look at me that way I mean come on look at the DNA!!!



    snoitseuq ksa



    Fellowship




    You know fellowship, I believe you might just have a PhD there.



    You could prove that there are two completely different sets of "building blocks", one for "living, breathing" creatures, and another set for fruits. You would have to show how that came about, but I have no doubt that someone with your grasp on science could do it.



    What about legumes? You might want to save those for the post-doc, or the afternoon snack, which ever comes first.
  • Reply 17 of 56
    toweltowel Posts: 1,479member
    Quote:

    We share half our genes with the banana. One can only guess (with a fertile imagination) what the common ancestor between people and bananas looked like! In addition, there are fish that have 40% the same DNA as people, but hopefully no evolutionist would claim that the fish are 40% human or people are half bananas. [/B]



    You're comparing, erm, Apple and Oranges there. If you're talking "genes" we probably share 90-95% of our genes with chimps. If you compare "DNA in genes", we're 98% identical to chimps, and 40% identical to fish sounds reasonable. Most genes in baker's yeast, to take a biologist's favorite, have a counterpart in humans. Often that one gene in yeast has branched into several families, each with multiple closely related human genes. Eukaryotes in general, from yeast to worms to mice to humans, all look recognizably similar to each other. That's why we spend to much money studying "model organisms": yeast, molds, flies, worms, frogs, zebrafish, mice, rats, etc.



    There is, of course, a common ancestor for humans and bananas - somewhere way back in the mists of time before there were plants and animals, when the most complicated organisms on earth were single-celled. Before one group of cells got cell walls and chloroplasts, and one group got mitochondria. Still, no one claims that people are half bananas, though many people think creationists are all bananas.
  • Reply 18 of 56
    enaena Posts: 667member
    <chief engineer impersonation>



    Fellowship!!! Dommitt mon!!! Ye canna do this!!! -If ye fool around w?an evolutionist's core beliefs, the whole things gonna blow!!



    </chief engineer impersonation>
  • Reply 19 of 56
    xenuxenu Posts: 204member
    Quote:

    Originally posted by ena

    <chief engineer impersonation>



    Fellowship!!! Dommitt mon!!! Ye canna do this!!! -If ye fool around w?an evolutionist's core beliefs, the whole things gonna blow!!



    </chief engineer impersonation>




    Core belief? Oh, you mean a judgement made on the basis of experimental evidence?



    I wonder where rocks fit into all of this?

    In the pointy bit?
  • Reply 20 of 56
    keyboardf12keyboardf12 Posts: 1,379member
    So i was watching the discovery channel last night and watch "walking with cavemen" very well done and educational.



    this thread cracks me up.
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