This fits with the evolutionary relationships we had deduced from other evidence, that we share a common ancestor with chimpanzees most recently, then gorillas and then orangutans.
And how did you deduce that?
Presupposition -> Assumption -> presumption.
This is like saying the finding footprints that match the shoes of the suspect and are covered in the victim's blood leading from the scene of the crime all the way to the suspect's home is deduced by presupposition.
It goes:
Develop a model -> Hypothesize what we would expect to find were the given model accurate -> Find it.
Do you not understand yet what I am trying to get through to you?
The many things scientists are claiming, are based on what they presume to be true based on the assumptions made from the little circumstantial evidence available to them.
This is also not true. Were evolution false, there would be no reason whatsoever for the fossil record to be in the state it's in, or for the common genetic lineage that links all living things. If evolution weren't true, neither of these things would be so.
Ever since Watson and Crick discovered the double helix structure of DNA back in the 1950s, scientists have been debating what extent of the genome is responsible for making you you – and now an evolutionary biologist says the answer to the riddle lies in some basic math.
Dan Graur from the University of Houston calculates that the functional portion of the human genome probably constitutes only about 10 to 15 percent of our overall DNA, with an upper limit of 25 percent.
The rest of our genome – somewhere between around 75 to 90 percent of our DNA – is what's called junk DNA: not necessarily harmful or toxic genetic matter, but useless, garbled nucleotide sequences that aren't functional in terms of encoding proteins that spur all the important chemical reactions going off inside our bodies.
The rationale for Graur's model is based on the way mutations creep into DNA, and how as a species we weed these mutations out for the benefit of all.
These kinds of genetic variants, called deleterious mutations, appear in our genome over time, subtly shifting or reordering the four chemical bases that make up DNA – adenine, cytosine, guanine and thymine – in parts of our genetic code.
When mutations take place in junk DNA, they're considered neutral – since that genetic code doesn't do anything, anyway – but when mutations occur to our functional, defining DNA, they can often be harmful and even ultimately lethal, as they mess up the instructions that code for healthy tissue and biological processes.
On that basis, it's better for our evolutionary prospects if less of our DNA is functional, because less of it is then exposed to the risk of mutation and the increased chances of early death it invites.
In Graur's calculations, given the risk of deleterious mutations to the survival of the species on one hand – and the known stability of population and reproduction rates throughout human history on the other – the limit of functional DNA has to be very low.
Otherwise dangerous mutations would keep stacking up, meaning we'd have to produce impossibly huge numbers of offspring for the small percentage of healthy bubs to survive.
"Under the assumption of 100 percent functionality and the range of deleterious mutation rates used in this paper, maintaining a constant population size would necessitate that each couple on average produce a minimum of 24 and a maximum of 5 × 1053 children," he writes in his paper.
Of course, nobody really other than creationists is suggesting that we carry around zero junk DNA, but a huge 2012 study called the Encyclopaedia of DNA Elements (ENCODE) project did claim that as much as 80 percent of human DNA was functional.
That study was controversial – partly because many scientists claimed that the ENCODE definition of 'functional' was too broad.
Human Genome 2.0: ENCODE project debunks ‘junk’ DNA DNA previously written off as junk actually acts as a lever controlling genetic activity, leading to health or illness, reveals a massive new genetic mapping project.
So just 1% of the genome, considered to be non-functioning, was found to be 80% functional.
Pseudogene Because pseudogenes were initially thought of as the last stop for genomic material that could be removed from the genome, they were often labeled as junk DNA.
Pseudogenes are sometimes difficult to identify and characterize in genomes, because the two requirements of homology and loss of functionality are usually implied through sequence alignments rather than biologically proven.
Pseudogenes for RNA genes are usually more difficult to discover as they do not need to be translated and thus do not have "reading frames".
Pseudogenes can complicate molecular genetic studies. For example, amplification of a gene by PCR may simultaneously amplify a pseudogene that shares similar sequences. This is known as PCR bias or amplification bias. Similarly, pseudogenes are sometimes annotated as genes in genome sequences.
Processed pseudogenes often pose a problem for gene prediction programs, often being misidentified as real genes or exons. It has been proposed that identification of processed pseudogenes can help improve the accuracy of gene prediction methods.
Recently 140 human pseudogenes have been shown to be translated. However, the function, if any, of the protein products is unknown.
Pseudogenes Noncoding regions of human genome in general were thought to be nonfunctional and “junk,” or of no purpose DNA. Nowadays, scientists are conceding that junk DNA terminology is far from true since recent studies indicate that they have some regulatory roles. This work focuses on pseudogenes of junk DNA.
The shared mutations in different organisms are thought to depend on common descent or evolutionary ancestry
Conclusion
I could have used many more examples, but it's long enough as it is.
I just highlighted these in the hope it will make my point clear enough for you to understand.
If you are a scientist, I do not fault you for doing your work. By all means, do your work as best you know how.
I understand that scientists make many assumptions, some without any particular or specific evidence, but when they do gather evidence, they do they best to fit this evidence into a naturalistic understanding.
I believe, based on what I have seen, the evidence - how ever little, or insufficient - is interpreted to fit a presupposition... actually, a presumption.
This is based on my observation, and experience... especially where the Darwinian view is concerned.
This is even seen in the assumptions made for millions of years required for XYZ.
Flash vaporization during earthquakes evidenced by gold deposits
Much of the world’s known gold has been derived from arrays of quartz veins. The veins formed during periods of mountain building that occurred as long as 3 billion years ago, and were deposited by very large volumes of water that flowed along deep, seismically active faults. The veins formed under fluctuating pressures during earthquakes, but the magnitude of the pressure fluctuations and their influence on mineral deposition is not known.
Earthquakes Make Gold Veins in an Instant
Scientists have long known that veins of gold are formed by mineral deposition from hot fluids flowing through cracks deep in Earth’s crust. But a study published today in Nature Geoscience has found that the process can occur almost instantaneously — possibly within a few tenths of a second.[/SPOILER]
I understand that you accept this system, where you cannot prove these claims, but you believe the best opinions offered in support of those claims.
If those opinions you argue for so strongly, became history the next week, month, or year, you would argue just as strongly for the newly accepted opinion.
That's your system of belief. I understand.
Mine is different, and I understand that you don't accept it.
However, each of us has to weight the evidence, and decide what to believe.
The gauge I use for measuring truth, does not change, and adjust. Rather, it often turns out, that discoveries that seem to be true, measure up correctly, to this gauge.
There is a lot that scientists are in the dark about, regarding the genome. Even their best instruments do not give accurate reading.
I hope I have explained clearly, and you understand.
One day, I think things will become clearly evident, to be undeniable.
That's not the case with your belief, apparently.
Thank you.
And how did you deduce that?
Presupposition -> Assumption -> presumption.
Do you not understand yet what I am trying to get through to you?
The many things scientists are claiming, are based on what they presume to be true based on the assumptions made from the little circumstantial evidence available to them.
I'm not sure you understand the concept of scientific evidence. If you have a hypothesis or theory, you go looking, via observation or experiment, for facts that either support it or potentially falsify it, or at least call it into question.
When we look at the human genome we see broken versions of genes that function in other creatures. That in itself is evidence of relatedness, and in this context we already have other evidence that points to the same relationships. When we add in the details about having the same inactivating mutations, we can construct a relationship model based only on that evidence. When that model matches the model we built using different evidence, we have strong confirmatory evidence for our theory.
This by itself would be good evidence of the relationships but when it's added to all the other evidence, it becomes all but certain.
Perhaps it's because nobody has come up with any. You haven't even tried to explain how the examples I've given you could be explained by special creation. The other problem is that special creation isn't a scientific hypothesis. A creator could have created things in literally any way at all - so how can there be evidence for it, let alone any opportunity to falsify it?
The creationists' problem is that evolution is supported by evidence (such as the examples I have given) and the more evidence for that, the more dishonest a creator would have to be.
By the way, when you speak of common ancestor in relation to human and chimp, etc., you are referring to common ancestry all the way to LUCA. Isn't that true?
Questions like this again make me wonder if you even get the process. The evidence in these examples, only provides evidence for a common ancestor of humans, orangutans, chimpanzees, and gorillas, or them and chickens if you include the other example, you would need to consider more evidence (and different kinds of evidence) to get back to LUCA.
I'm not sure you understand the concept of scientific evidence. If you have a hypothesis or theory, you go looking, via observation or experiment, for facts that either support it or potentially falsify it, or at least call it into question.
I'm not sure you understand how bias works in human beings... even in scientists.
The way you described is perhaps the way things ought to work. It is not how things work at all times. Scientists attacked over claim that 'junk DNA' is vital to life ...this idea is now the subject of an astonishingly vitriolic attack from other scientists, who say that Encode's "absurd" ideas are the work of people who know nothing about evolutionary biology. "News concerning the death of junk DNA has been greatly exaggerated," they insist.
The row divides scientists over the most fundamental of questions – is most of our DNA devoid of purpose or does it play a major role in our cells?
"Everything that Encode claims is wrong. Their statistics are horrible, for a start," the lead author of the paper, Professor Dan Graur, of Houston University, Texas, told the Observer. "This is not the work of scientists. This is the work of a group of badly trained technicians."
When the human genome was sequenced in 2000, only 26,000 genes appeared to be directing the manufacture of proteins and growth control, and 98% of our DNA was written off.
But Encode researchers claimed to have identified more than 10,000 new genes and suggested that up to 18% of our DNA is responsible for regulating other genes. They said about 80% of DNA had a biochemical function.
This is dismissed as "absurd" by Graur and others, including scientists from Johns Hopkins University in Baltimore.They accuse Encode of using "analytical methods that yield biased errors and inflate estimates of functionality" and say it reveals a basic misunderstanding of evolutionary biology.
But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."
Biologist who don't know basic biology. Wow. Not only that, they accuse scientists of being dishonest for monetary gain. Must be Creationist with an agenda. No wonder they don't know simple biology. Sounds familiar.
'Junk' DNA Has Important Role, Researchers Find Researchers who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism.They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.
Scientists have called it "junk DNA." They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?
It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load. "The transposons actually perform a central role for the cell," said Laura Landweber, a professor of ecology and evolutionary biology at Princeton and an author of the study. "They stitch together the genes in working form." The work appeared in the May 15 edition of Science.
Wow. We don't understand it, so it must be senseless worthless garbage. Non-coding DNA - Wikipedia Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "non-coding DNA" instead; "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage.
Leslie Orgel and Francis Crick wrote that junk DNA has "little specificity and conveys little or no selective advantage to the organism". The term occurs mainly in popular science and in a colloquial way in scientific publications, and it has been suggested that its connotations may have delayed interest in the biological functions of non-coding DNA. Several lines of evidence indicate that some "junk DNA" sequences are likely to have unidentified functional activity and that the process of exaptation of fragments of originally selfish or non-functional DNA has been commonplace throughout evolution.
___________________________
...most of the difference in genome size is not due to variation in amount of coding DNA, rather, it is due to a difference in the amount of non-coding DNA.
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans.Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.
This is your belief system.
Please forgive the length. These are specific points I am highlighting.
When we look at the human genome we see broken versions of genes that function in other creatures. That in itself is evidence of relatedness, and in this context we already have other evidence that points to the same relationships. When we add in the details about having the same inactivating mutations, we can construct a relationship model based only on that evidence. When that model matches the model we built using different evidence, we have strong confirmatory evidence for our theory.
This by itself would be good evidence of the relationships but when it's added to all the other evidence, it becomes all but certain.
Pointing to things you know very little about, does undermine what you assume to be supportive evidence for your claims.
In fact, pointing to things you don't know, and claiming that you know, is fraud. Calling it science is worst.
Perhaps it's because nobody has come up with any. You haven't even tried to explain how the examples I've given you could be explained by special creation. The other problem is that special creation isn't a scientific hypothesis. A creator could have created things in literally any way at all - so how can there be evidence for it, let alone any opportunity to falsify it?
The creationists' problem is that evolution is supported by evidence (such as the examples I have given) and the more evidence for that, the more dishonest a creator would have to be.
All Creationist have to do is point out one basic fact. That you have so little understanding of what you are assuming to know, demonstrates that you are basing all your conclusions on assumptions, guesswork, and speculation - aka presuming.
Then we can simply point to the fact that believers in evolution write off, or dismiss as useless, anything that they don't understand. This blocks or restricts any consideration of intelligent design.
We don't have to go into details. The believers in the god science, are in the dark.
Questions like this again make me wonder if you even get the process. The evidence in these examples, only provides evidence for a common ancestor of humans, orangutans, chimpanzees, and gorillas, or them and chickens if you include the other example, you would need to consider more evidence (and different kinds of evidence) to get back to LUCA.
I am not really asking a question. It was rhetorical.
I am saying basically, concluding that there is evidence for a common ancestor of humans, orangutans, chimpanzees, is the same as concluding that all life came from LUCA. Actually it is as I said previously - circular reasoning that starts with a presupposition, and ends with a presumption.
No, it won't be falsified, because it is modified to fit the evidence that would falsify it. It's the most flexible idea on the planet.
It's a good thing for anyone to keep the law. The best teaching is teaching by example. But certainly he was not unique. nPeace, the heart of Christianity is that Jesus is unique, and that is just wrong. That's why I'm a Jew and not a Christian.
It's a good thing for anyone to keep the law. The best teaching is teaching by example. But certainly he was not unique. nPeace, the heart of Christianity is that Jesus is unique, and that is just wrong. That's why I'm a Jew and not a Christian.
I'm not sure you understand how bias works in human beings... even in scientists.
The way you described is perhaps the way things ought to work. It is not how things work at all times.
...
This is your belief system.
Please forgive the length. These are specific points I am highlighting.
This is observation that very much supports the theory of common ancestry for the species in question. That means it is what we would expect if the theory is true and not what we'd expect if it were false. That's what scientific evidence is.
You still haven't even tried to put forward an alternative hypothesis that might be consistent with it...
Pointing to things you know very little about, does undermine what you assume to be supportive evidence for your claims.
In fact, pointing to things you don't know, and claiming that you know, is fraud. Calling it science is worst.
This is a total misrepresentation. We know what the functioning versions of the genes look like and we can find versions that have mutations that are known to happen and stop that function. That is evidence regardless of what the rest of the "junk DNA" might be doing. It actually says in the article I linked that the one of the few response to pseudogene evidence from the ID and creationists was to attempt to conflate the problem with junk DNA in general - which is dishonest.
All Creationist have to do is point out one basic fact. That you have so little understanding of what you are assuming to know, demonstrates that you are basing all your conclusions on assumptions, guesswork, and speculation - aka presuming.
Which is basically called "bearing false witness". We have the evidence we have and it stands despite the questions about other parts of the genome. We actually know a lot about genetics from experiment and observations, we can edit DNA and observe the result, and we've constructed entirely synthetic genomes (link). We don't need to know everything to draw conclusions - science would never get anywhere if we tried to do it on that basis.
I am saying basically, concluding that there is evidence for a common ancestor of humans, orangutans, chimpanzees, is the same as concluding that all life came from LUCA.
No, it's the scientific method. You form a hypothesis, then you try to test it by looking at the evidence and seeing if it matches the hypothesis or doesn't. That's how science always works. That's what is done with evolution. What I've given you here is just one tiny glimpse of the tests.
Nonsense. There are multiple ways in which it could be falsified, fossil rabbits in the Precambrian being a famous example but, as I said before, if we'd have found distinctly different genetics that divided life up into "kinds", that would have falsified Universal common ancestry.
You highlighting an irrelevant controversy that exists because we don't have enough evidence yet. Distraction?
This is observation that very much supports the theory of common ancestry for the species in question. That means it is what we would expect if the theory is true and not what we'd expect if it were false. That's what scientific evidence is.
You still haven't even tried to put forward an alternative hypothesis that might be consistent with it...
This is a total misrepresentation. We know what the functioning versions of the genes look like and we can find versions that have mutations that are known to happen and stop that function. That is evidence regardless of what the rest of the "junk DNA" might be doing. It actually says in the article I linked that the one of the few response to pseudogene evidence from the ID and creationists was to attempt to conflate the problem with junk DNA in general - which is dishonest.
Which is basically called "bearing false witness". We have the evidence we have and it stands despite the questions about other parts of the genome. We actually know a lot about genetics from experiment and observations, we can edit DNA and observe the result, and we've constructed entirely synthetic genomes (link). We don't need to know everything to draw conclusions - science would never get anywhere if we tried to do it on that basis.
No, it isn't - obviously.
No, it's the scientific method. You form a hypothesis, then you try to test it by looking at the evidence and seeing if it matches the hypothesis or doesn't. That's how science always works. That's what is done with evolution. What I've given you here is just one tiny glimpse of the tests.
Nonsense. There are multiple ways in which it could be falsified, fossil rabbits in the Precambrian being a famous example but, as I said before, if we'd have found distinctly different genetics that divided life up into "kinds", that would have falsified Universal common ancestry.
I'm not trying to distract you. This is all related.
What is it you agree to, that you don't "have enough evidence of yet"?
Do you know which segments of DNA are responsible for the function and survival of an organism?
This doesn't really make sense. What are you trying to ask? Genes, or rather, combinations of genes, give rise to traits and what traits are useful for survival depends on the environment and on other traits that may be selected for. For example, if an enhanced sense of smell were important to our ancestors, the olfactory receptor genes, which we were speaking of, would have been persevered by natural selection, as it is, their loss was clearly not significant to survival at the time.
The existence of these pseudo or fossil genes is an observation that supports the theory of evolution by natural selection and is difficult to fit with the idea of special creation. Remember that the idea that populations gain new traits and lose ones that are not helpful to survival, predates genetics. The discovery of fossil genes is exactly what we would expect, given evolution by natural selection and the facts about how genes work. This is what is called "evidence".
What, if anything, some of the "junk DNA" is doing.
This doesn't really make sense. What are you trying to ask? Genes, or rather, combinations of genes, give rise to traits and what traits are useful for survival depends on the environment and on other traits that may be selected for. For example, if an enhanced sense of smell were important to our ancestors, the olfactory receptor genes, which we were speaking of, would have been persevered by natural selection, as it is, their loss was clearly not significant to survival at the time.
The existence of these pseudo or fossil genes is an observation that supports the theory of evolution by natural selection and is difficult to fit with the idea of special creation. Remember that the idea that populations gain new traits and lose ones that are not helpful to survival, predates genetics. The discovery of fossil genes is exactly what we would expect, given evolution by natural selection and the facts about how genes work. This is what is called "evidence".
Sorry. I asked that question wrong. Pardon my mistake. That should be....
Do you know which segments of the gene are responsible for the function and survival of an organism?
I'm not sure you understand how bias works in human beings... even in scientists.
The way you described is perhaps the way things ought to work. It is not how things work at all times. Scientists attacked over claim that 'junk DNA' is vital to life ...this idea is now the subject of an astonishingly vitriolic attack from other scientists, who say that Encode's "absurd" ideas are the work of people who know nothing about evolutionary biology. "News concerning the death of junk DNA has been greatly exaggerated," they insist.
The row divides scientists over the most fundamental of questions – is most of our DNA devoid of purpose or does it play a major role in our cells?
"Everything that Encode claims is wrong. Their statistics are horrible, for a start," the lead author of the paper, Professor Dan Graur, of Houston University, Texas, told the Observer. "This is not the work of scientists. This is the work of a group of badly trained technicians."
When the human genome was sequenced in 2000, only 26,000 genes appeared to be directing the manufacture of proteins and growth control, and 98% of our DNA was written off.
But Encode researchers claimed to have identified more than 10,000 new genes and suggested that up to 18% of our DNA is responsible for regulating other genes. They said about 80% of DNA had a biochemical function.
This is dismissed as "absurd" by Graur and others, including scientists from Johns Hopkins University in Baltimore.They accuse Encode of using "analytical methods that yield biased errors and inflate estimates of functionality" and say it reveals a basic misunderstanding of evolutionary biology.
But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."
Biologist who don't know basic biology. Wow. Not only that, they accuse scientists of being dishonest for monetary gain. Must be Creationist with an agenda. No wonder they don't know simple biology. Sounds familiar.
'Junk' DNA Has Important Role, Researchers Find Researchers who have been studying the genome of a pond organism have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism.They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.
Scientists have called it "junk DNA." They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?
It all happens very quickly. Genes called transposons in the single-celled pond-dwelling organism Oxytricha produce cell proteins known as transposases. During development, the transposons appear to first influence hundreds of thousands of DNA pieces to regroup. Then, when no longer needed, the organism cleverly erases the transposases from its genetic material, paring its genome to a slim 5 percent of its original load. "The transposons actually perform a central role for the cell," said Laura Landweber, a professor of ecology and evolutionary biology at Princeton and an author of the study. "They stitch together the genes in working form." The work appeared in the May 15 edition of Science.
Wow. We don't understand it, so it must be senseless worthless garbage. Non-coding DNA - Wikipedia Though the fruitfulness of the term "junk DNA" has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and though some have recommended using more neutral terminology such as "non-coding DNA" instead; "junk DNA" remains a label for the portions of a genome sequence for which no discernible function has been identified and that through comparative genomics analysis appear under no functional constraint suggesting that the sequence itself has provided no adaptive advantage.
Leslie Orgel and Francis Crick wrote that junk DNA has "little specificity and conveys little or no selective advantage to the organism". The term occurs mainly in popular science and in a colloquial way in scientific publications, and it has been suggested that its connotations may have delayed interest in the biological functions of non-coding DNA. Several lines of evidence indicate that some "junk DNA" sequences are likely to have unidentified functional activity and that the process of exaptation of fragments of originally selfish or non-functional DNA has been commonplace throughout evolution.
___________________________
...most of the difference in genome size is not due to variation in amount of coding DNA, rather, it is due to a difference in the amount of non-coding DNA.
In 2013, a new "record" for the most efficient eukaryotic genome was discovered with Utricularia gibba, a bladderwort plant that has only 3% non-coding DNA and 97% of coding DNA. Parts of the non-coding DNA were being deleted by the plant and this suggested that non-coding DNA may not be as critical for plants, even though non-coding DNA is useful for humans.Other studies on plants have discovered crucial functions in portions of non-coding DNA that were previously thought to be negligible and have added a new layer to the understanding of gene regulation.
This is your belief system.
Please forgive the length. These are specific points I am highlighting.
What you see, and what you interpret are two different things.
...but this is science. Or is it Scientism.
Pointing to things you know very little about, does undermine what you assume to be supportive evidence for your claims.
In fact, pointing to things you don't know, and claiming that you know, is fraud. Calling it science is worst.
All Creationist have to do is point out one basic fact. That you have so little understanding of what you are assuming to know, demonstrates that you are basing all your conclusions on assumptions, guesswork, and speculation - aka presuming.
Then we can simply point to the fact that believers in evolution write off, or dismiss as useless, anything that they don't understand. This blocks or restricts any consideration of intelligent design.
We don't have to go into details. The believers in the god science, are in the dark.
I am not really asking a question. It was rhetorical.
I am saying basically, concluding that there is evidence for a common ancestor of humans, orangutans, chimpanzees, is the same as concluding that all life came from LUCA. Actually it is as I said previously - circular reasoning that starts with a presupposition, and ends with a presumption.
No, it won't be falsified, because it is modified to fit the evidence that would falsify it. It's the most flexible idea on the planet.
Sorry. I asked that question wrong. Pardon my mistake. That should be....
Do you know which segments of the gene are responsible for the function and survival of an organism?
First of all, the work itself is just fine and was well done. The problems came in when the project leads started overselling their results to the media. You see, in their research they looked for sequences of DNA that showed "biochemical activity" (which is fine), and everything that showed any such activity they declared to be "functional" (which isn't fine). IOW, if the DNA sequence did anything at all, no matter what it was actually doing, the ENCODE folks labelled it as "functional", and when they added up all those "functional" elements they got their "80% of the human genome is functional" conclusion, which they repeated to the media, which led to the breathless headlines and media buzz.
The problem there is that geneticists already knew quite well that just because a segment of DNA "does something", that doesn't mean that "something" actually contributes to the function of the cell/organism. I won't get too detailed here, but a good example is how with some protein-coding sequences, they make the protein only to have the protein immediately broken down and digested inside the cell. So the actual protein never does anything. But under ENCODE's criteria, the DNA sequence that coded for that protein was included in the "functional" category, even though the protein was destroyed as soon as it was made. That's what made their colleagues angry.
If you take anything away from this, it should be that just because a DNA sequence "does something", that doesn't necessarily mean that "something" is biologically meaningful.
First of all, the work itself is just fine and was well done. The problems came in when the project leads started overselling their results to the media. You see, in their research they looked for sequences of DNA that showed "biochemical activity" (which is fine), and everything that showed any such activity they declared to be "functional" (which isn't fine). IOW, if the DNA sequence did anything at all, no matter what it was actually doing, the ENCODE folks labelled it as "functional", and when they added up all those "functional" elements they got their "80% of the human genome is functional" conclusion, which they repeated to the media, which led to the breathless headlines and media buzz.
The problem there is that geneticists already knew quite well that just because a segment of DNA "does something", that doesn't mean that "something" actually contributes to the function of the cell/organism. I won't get too detailed here, but a good example is how with some protein-coding sequences, they make the protein only to have the protein immediately broken down and digested inside the cell. So the actual protein never does anything. But under ENCODE's criteria, the DNA sequence that coded for that protein was included in the "functional" category, even though the protein was destroyed as soon as it was made. That's what made their colleagues angry.
If you take anything away from this, it should be that just because a DNA sequence "does something", that doesn't necessarily mean that "something" is biologically meaningful.
That's fine. I just hope you now understand that "does something" doesn't necessarily equate to "functional" when talking about things like "junk DNA". To be clear, there are most certainly segments of the human genome that are "junk", in that they're not at all relevant to the function of the organism.
Even under ENCODE's questionable criteria, a full 20% of the human genome was non-functional.
That's fine. I just hope you now understand that "does something" doesn't necessarily equate to "functional" when talking about things like "junk DNA". To be clear, there are most certainly segments of the human genome that are "junk", in that they're not at all relevant to the function of the organism.
Even under ENCODE's questionable criteria, a full 20% of the human genome was non-functional.
Q. Hmmm. Let’s move onto the science. I don’t buy that 80% of the genome is functional.
A. It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e, if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.
Q. So remind me which one do you think is “functional”?
A. Back to that word “functional”: There is no easy answer to this. In ENCODE we present this hierarchy of assays with cumulative coverage percentages, ending up with 80%. As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising.
However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNArotein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons, this is surprisingly high for many people – certainly it was to me!
In addition, in this phase of ENCODE we did sample broadly but nowhere near completely in terms of cell types or transcription factors. We estimated how well we have sampled, and our most generous view of our sampling is that we’ve seen around 50% of the elements. There are lots of reasons to think we have sampled less than this (e.g., the inability to sample developmental cell types; classes of transcription factors which we have not seen). A conservative estimate of our expected coverage of exons + specific DNArotein contacts gives us 18%, easily further justified (given our sampling) to 20%
Because pseudogenes 
