Junk DNA and Intelligent Design
A big topic in the evolution/creationism debate relates to the concept of so-called "Junk DNA". IDists pretend that they predicted junk DNA would have a function, and they pretend that evolution predicts it would not. Therefore, so they say, the recent findings that much of junk DNA has a function supports ID and refutes evolution.
Spoiler alert: They are lying.
What Is Junk DNA?
Junk DNA refers to any DNA that does not code for proteins, of which there is a lot. It is also called non-coding DNA, which is perhaps a better term. About 98% of human DNA is non-coding. A good primer can be found here.
This web page has an image that compares the number of base-pairs in various animal species, from 1.1 billion in Anne's humming bird, to 3.4 in humans, to 4.3 in a sea cucumber, all the way up to 8.22 in Red viscacha rat. A plant, Paris japonica, has 150 billion base-pairs, while Polychaos dubium, a freshwater amoeboid, may have 670 base-pairs, about 200 times more than humans.
You might like to think at this point what ID predicts for genome size, given ID is all about complexity and information, and insists there is no junk DNA!
Is anyone going to pretend that ID predicts the onion genome is five times the size of the human genome?
This web page has an image that compares the number of base-pairs in various animal species, from 1.1 billion in Anne's humming bird, to 3.4 in humans, to 4.3 in a sea cucumber, all the way up to 8.22 in Red viscacha rat. A plant, Paris japonica, has 150 billion base-pairs, while Polychaos dubium, a freshwater amoeboid, may have 670 base-pairs, about 200 times more than humans.
You might like to think at this point what ID predicts for genome size, given ID is all about complexity and information, and insists there is no junk DNA!
Is anyone going to pretend that ID predicts the onion genome is five times the size of the human genome?
Some Non-Coding DNA Has Function
About fifty years ago, it was assumed that this non-coding DNA had no function at all, but over the years - and especially with the ENCODE project - scientists have come to realise that at least some non-coding DNA has some function.
One such function is to produce RNA that regulates protein production in some way (in contrast to coding DNA, which produces RNA that directly codes for a protein).
One such function is to produce RNA that regulates protein production in some way (in contrast to coding DNA, which produces RNA that directly codes for a protein).
But this is not new. See for example:
"The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes", S Lin, AD Riggs AD, Cell. 1975 Feb;4(2):107-11.
... We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions. ...
"A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins", E Zuckerkandl E, Mol Biol Rep. 1981 May 22;7(1-3):149-58.
It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. ...
Note that these pre-date the whole ID movement. Scientists - some at least - believed junk DNA had a function before ID was even invented.
Transposons
About 44% of human DNA is made up of transposons - also called Transposable Elements (TEs). These are DNA sequences that can move around. I think the timescale for such a move is on the order of months to years, so you have probably had this happen several times, but if anyone can confirm or deny, that would be great!.
One sequence, called the "Alu element", appears over a millions times in human DNA, making up 15 to 17% of our DNA. The Alu element is considered parasitic as its primary function appears to be to replicate itself within the genome. That said, it does play some role in gene regulation and expression.
Alu element insertion happens a couple of hundred times in a million years, and there is no known mechanism for deletion, which makes it interesting for evolutionists. Of the million or so sequences in the human genome, only about 7000 are unique to humans, and so will have entered the genome since the human/chimp split.
These articles discuss the evolution of the Alu element from the time of the rodent/primate split up to modern man.
https://www.nature.com/articles/nature04072
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-12-236
https://www.pnas.org/content/100/22/12787
Tranposons can cause diseases such as haemophilia and porphyria, and cells have a defence against transposons.
I would be interested to hear what ID says about transposons. Why is the Alu sequence so prolific; why did God... er, sorry, the unknown designer give us over a million? Why do we see this pattern of distribution in primates? If transposons were designed into humans, why did the designer also design a defend against transposons into us?
IDists have no answer, so just ignore questions like this. ID is pseudo-science.
One sequence, called the "Alu element", appears over a millions times in human DNA, making up 15 to 17% of our DNA. The Alu element is considered parasitic as its primary function appears to be to replicate itself within the genome. That said, it does play some role in gene regulation and expression.
Alu element insertion happens a couple of hundred times in a million years, and there is no known mechanism for deletion, which makes it interesting for evolutionists. Of the million or so sequences in the human genome, only about 7000 are unique to humans, and so will have entered the genome since the human/chimp split.
These articles discuss the evolution of the Alu element from the time of the rodent/primate split up to modern man.
https://www.nature.com/articles/nature04072
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-12-236
https://www.pnas.org/content/100/22/12787
Tranposons can cause diseases such as haemophilia and porphyria, and cells have a defence against transposons.
I would be interested to hear what ID says about transposons. Why is the Alu sequence so prolific; why did God... er, sorry, the unknown designer give us over a million? Why do we see this pattern of distribution in primates? If transposons were designed into humans, why did the designer also design a defend against transposons into us?
IDists have no answer, so just ignore questions like this. ID is pseudo-science.
Pseudogenes
Pseudogenes are genes that are broken - a mutation has stopped the gene working, but its remnants are still there in the genome. A great example is the pseudogene for vitamin C.
Pseudogenes may still have function. What characterises them is that they have lost their original function. We can see the original function by comparison with other organisms. Cats, for example, have a working gene, and so can produce vitamin C. Humans, like other primates, have approximately the same sequence, but mutations mean it does not actually work.
I do not know if the pseudogene for vitamin C has another function, but it is likely it does, given it is so well preserved.
Pseudogenes may still have function. What characterises them is that they have lost their original function. We can see the original function by comparison with other organisms. Cats, for example, have a working gene, and so can produce vitamin C. Humans, like other primates, have approximately the same sequence, but mutations mean it does not actually work.
I do not know if the pseudogene for vitamin C has another function, but it is likely it does, given it is so well preserved.
How does ID explain the distribution of the vitamin C pseudogene? It cannot, so IDists just ignore the question.
Evolution's Playground
An important use for DNA sequences that have no use is as a sandbox for evolution. These are sections that can freely mutate without a deleterious effect on the organism, but which might just happen to give some useful new gene. The fact that they can mutate indicates they have no other function! This article in Nature describes how new genes can arise, and does mention new genes from transposons.
In a sense, then, all DNA necessarily has a use. I would suggest, however, that this does not count as a use when discussing ID - if it does, then the evolutionary prediction is that all DNA is useful.
In a sense, then, all DNA necessarily has a use. I would suggest, however, that this does not count as a use when discussing ID - if it does, then the evolutionary prediction is that all DNA is useful.
Predictions From ID
IDists say that they predicted there is no junk DNA, but I would be curious to know the details.
Are they saying that all DNA has a function (and not just as evolution's playground)? That is not what the evidence currently points to, but could nevertheless be the case.
Is this a prediction in the sense of an intuition they have? Or is it a scientific prediction in the sense of a necessary consequence of their hypothesis? If the later, exactly what is the hypothesis, and where does the prediction come from?
Are they saying that all DNA has a function (and not just as evolution's playground)? That is not what the evidence currently points to, but could nevertheless be the case.
Is this a prediction in the sense of an intuition they have? Or is it a scientific prediction in the sense of a necessary consequence of their hypothesis? If the later, exactly what is the hypothesis, and where does the prediction come from?
As usual, IDists ignore these questions.
ID is about presenting the façade of science; it is not actual science.
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