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Bye bye, cultist."I will need to see a reference for that. In the rest of the world, Covid-19 often produces long-term effects, some of which may be permanent."
I am just talking to you, I am not your mama.
@tas8831
Your opening post got me thinking about analogies even if most of it is beyond my understanding.
I've occasionally heard a creationist argument about how DNA is a code and therefore must have an author. I often think about that and feel strongly that it doesn't pass the sniff test but I find it hard to parse exactly what is wrong with it. But I have some rough ideas.
It's easy to image a scientist saying at one time that DNA is like a code. And someone else interpreting that DNA is in fact a code. The problem I see is that the word 'like' in the English language has (too) many usages.
If I say "it looks like no one is here", then the situation is exactly what it looks like, no one is here.
If I say "that cat looks like a dog', then the situation is not what it looks like, because a cat is not a dog.
So if someone says that DNA is like a code, it's like the second example because DNA is not a code and a cat is not a dog.
Just because you can glean information out of DNA, does not make it a code, requiring an author. In the same way that tree rings are not a code. If you cut down a tree and count the rings, you can get information about the age of the tree. That does not make tree rings a code. Tree rings are the result of natural physical processes and do not require an author. The same is true for DNA.
I'm wondering if my reasoning is even in the ballpark of being correct.
Yeah, I agree.Strictly speaking, that is it. Unfortunately, as is often the case in science (especially when science is conveyed to/discussed by the public), words are often used more figuratively. 'Genetic code' is often used to refer to a gene, or the whole genome. This is incorrect, but many - even biologists - do it (and it drives me crazy). Dawkins explicitly refers to the DNA as 'digital code.' When he explains it, it makes sense, but then we have to deal with people running around saying 'a code needs a code-maker!'
I think the problem originates in the way we think - simplifying the complex, using heuristics and approximations, interpreting the unfamiliar in terms of the familiar - and our typically agency-based anthropocentric view of the world.Yeah, I agree.
The problem is firmly embedded in the language now too, (I think). I mean even the 'm' in 'mRNA' conjures up the image of some kind of secret, vital message being sent from one part of a cell to another. In this sense, the analogy itself, is driving the spread of the misconception, with the biologists themselves being responsible for that(?) Its akin to the notorious 'something from nothing' analogy in Cosmology ..
To help me better understand the argument, What is gene duplication, anyway? Is this the gene intrinsic to the living animal, being duplicated in the egg/sperm, or in the complete animal?OK, I will take one at a time as I am supposed to be doing real work... (see below)
Agreed.
Good thinking.
OK, I am probably guilty of that.But it comes from experience, as I have been on forums like this for more than 25 years off and on, and am pretty used to the sorts of objections that I can expect to encounter.
#1
This one is in response to this kind of scenario:
The dog ran fast. The dog ran fast.
That pair of sentences (or something very much like it) is the sort of 'analogy' I have seen from anti-evolutionists attempting to dismiss the notion that gene duplications can possibly be a good thing, and that is premised as best I can tell on the notion that 'repeating what is already there does not add new information, and (according to the 'information' mongers like Dembski) 'new information' is required for adaptation/evolution'. Because after all, writing those sentences twice in a row does not alter their impact or tell us anything more about the dog.
Gene duplication is a pretty common event, and the evidence indicates that it is the culprit behind the generation of most gene families. A gene family is a group of genes of very similar sequence, typically all right next to each other on a chromosome, within which individual genes have been erroneously copied during DNA synthesis and over time, the duplicates have accumulated mutational change. Some of these duplicates mutate out of functionality (these are called pseudogenes - still recognizable by their sequence, but not actively transcribed), others acquire similar but divergent function, and sometimes new functions altogether. The Beta Globin gene cluster is probably among the most studied of these gene families.
In other cases, the duplication events have occurred relatively recently, and the duplicates have generally not had time to accumulate sufficient DNA change to alter their function, but having an extra copy of a functioning gene can still affect physiology/phenotype. The paper cited and quoted below is an example of this, and shows that 'duplicating what s already there' does allow for adaptation, so the whole 'no new information'/'those sentences written twice make no sense' argument is rendered moot.
Human populations can vary in the number of copies of the gene for Amylase, a starch-digesting protein. Starch is an important source of glucose, our (animals) main source of "fuel" to make ATP in cells. Having additional copies of this gene increases the amount of Amylase produced, allowing for populations that have these duplicated genes to more readily digest starch and thus have more 'freed up fuel', making metabolic processes more efficient (among other things). And as is concluded in the abstract below, this appears to be an adaptive trait premised solely on having "more of what is already there."
Diet and the evolution of human amylase gene copy number variation
Abstract
Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch1,2,3. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis4. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number–variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.
To help me better understand the argument, What is gene duplication, anyway? Is this the gene intrinsic to the living animal, being duplicated in the egg/sperm, or in the complete animal?
(If in the complete animal, then, I guess I'm hearing you say that what we observe as differences between say, father and son, (besides the usual by way of the union of sperm and egg), is because of this process we have observed. At least some of the differences are because of the duplicate (but not exact) genes. Thus, mutation. And this is not what results in mutation, but is the mutation, with effects/results visible in the product.)
(Also, I'm hearing you say that if this is indeed a cause of such mutations, it is more likely that those genetics that lend themselves to use starch well, continue to produce results that lend themselves use starch better. Also, it sounds like the starch users have an advantage over the meat eaters in this regard?)
As far as argument goes, I don't know enough to argue the duplicate gene business anyway, yet here, if I'm reading right, "appears to be", and "allowing for...populations to more readily...", is still speculation, (or worse, confirmation bias —if it results in positive claim depending on suggestions the phenomenon raises to the observer.) Still, it sound like an intriguing phenomenon.
Supposing the suggestions to be true (i.e. more than mere suggestion), is there any indicator of usual size/ distance of mutation per generation, and therefore, of time it takes to go from one form to another? What I'm getting at, is how many useful mutations happen fast enough to accomplish the immense differences between say, a single-celled organism and modern human, in the few thousand/million years since life began? (I'm aware that this is apparently not the only source of useful reproducible mutation, so include those other sources/causes too, in the estimate). Yes, I realize this is jumping ahead, but it will be one question I would eventually need answered, even if I accepted every report / interpretation of phenomena studied and all the relevant data brought to bear.
OK, I will take one at a time as I am supposed to be doing real work... (see below)
Agreed.
Good thinking.
OK, I am probably guilty of that.But it comes from experience, as I have been on forums like this for more than 25 years off and on, and am pretty used to the sorts of objections that I can expect to encounter.
#1
This one is in response to this kind of scenario:
The dog ran fast. The dog ran fast.
That pair of sentences (or something very much like it) is the sort of 'analogy' I have seen from anti-evolutionists attempting to dismiss the notion that gene duplications can possibly be a good thing, and that is premised as best I can tell on the notion that 'repeating what is already there does not add new information, and (according to the 'information' mongers like Dembski) 'new information' is required for adaptation/evolution'. Because after all, writing those sentences twice in a row does not alter their impact or tell us anything more about the dog.
Gene duplication is a pretty common event, and the evidence indicates that it is the culprit behind the generation of most gene families. A gene family is a group of genes of very similar sequence, typically all right next to each other on a chromosome, within which individual genes have been erroneously copied during DNA synthesis and over time, the duplicates have accumulated mutational change. Some of these duplicates mutate out of functionality (these are called pseudogenes - still recognizable by their sequence, but not actively transcribed), others acquire similar but divergent function, and sometimes new functions altogether. The Beta Globin gene cluster is probably among the most studied of these gene families.
In other cases, the duplication events have occurred relatively recently, and the duplicates have generally not had time to accumulate sufficient DNA change to alter their function, but having an extra copy of a functioning gene can still affect physiology/phenotype. The paper cited and quoted below is an example of this, and shows that 'duplicating what s already there' does allow for adaptation, so the whole 'no new information'/'those sentences written twice make no sense' argument is rendered moot.
Human populations can vary in the number of copies of the gene for Amylase, a starch-digesting protein. Starch is an important source of glucose, our (animals) main source of "fuel" to make ATP in cells. Having additional copies of this gene increases the amount of Amylase produced, allowing for populations that have these duplicated genes to more readily digest starch and thus have more 'freed up fuel', making metabolic processes more efficient (among other things). And as is concluded in the abstract below, this appears to be an adaptive trait premised solely on having "more of what is already there."
Diet and the evolution of human amylase gene copy number variation
Abstract
Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch1,2,3. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis4. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number–variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.
I provided a link in the earlier response that explains it better than I could, but I will try.To help me better understand the argument, What is gene duplication, anyway?
Duplications can happen in any cell that is undergoing division, but if it happens in, say, a skin cell, it will not be passed on. When we talk about duplicated genes, these are genes that have been copied most likely during the production of a sperm or egg, so they could be passed on to offspring.Is this the gene intrinsic to the living animal, being duplicated in the egg/sperm, or in the complete animal?
In a way, yes. But the differences between father and son are more likely due to the recombined genes from the mother and father - differences themselves of which are produced via mutations of some sort.(If in the complete animal, then, I guess I'm hearing you say that what we observe as differences between say, father and son, (besides the usual by way of the union of sperm and egg), is because of this process we have observed. At least some of the differences are because of the duplicate (but not exact) genes.
If I am following you correctly, I think yes.Thus, mutation. And this is not what results in mutation, but is the mutation, with effects/results visible in the product.)
That sounds pretty correct.(Also, I'm hearing you say that if this is indeed a cause of such mutations, it is more likely that those genetics that lend themselves to use starch well, continue to produce results that lend themselves use starch better. Also, it sounds like the starch users have an advantage over the meat eaters in this regard?)
What you are seeing is the tentative language of science. Less speculation and more cautious/tentative conclusions.As far as argument goes, I don't know enough to argue the duplicate gene business anyway, yet here, if I'm reading right, "appears to be", and "allowing for...populations to more readily...", is still speculation, (or worse, confirmation bias —if it results in positive claim depending on suggestions the phenomenon raises to the observer.) Still, it sound like an intriguing phenomenon.
Kimura (famous population geneticist) calculated in 1961 that "the total amount of genetic information which has been accumulated since the beginning of the Cambrian epoch along the lineage leading to higher mammals may be of the order of one hundred million bits (10^8 bits)."Supposing the suggestions to be true (i.e. more than mere suggestion), is there any indicator of usual size/ distance of mutation per generation, and therefore, of time it takes to go from one form to another? What I'm getting at, is how many useful mutations happen fast enough to accomplish the immense differences between say, a single-celled organism and modern human, in the few thousand/million years since life began? (I'm aware that this is apparently not the only source of useful reproducible mutation, so include those other sources/causes too, in the estimate).
I'll do what I can, but I think you are going to have to drop that unilateral skepticism and realize that, given what you've been writing, admit that you were shall we say, a bit premature in your dismissal of evolution given your apparent lack of basic scientific understanding.Yes, I realize this is jumping ahead, but it will be one question I would eventually need answered, even if I accepted every report / interpretation of phenomena studied and all the relevant data brought to bear.
It's not that, though I suppose from your end it could be seen that way toward me, lol. I just have not gotten from you anything but this one argument against something that more-knowledgeable-on-the-subject-than-I-am creationists argue. While you may be right and win that argument, you haven't convinced me of anything that I would need to reject creationism and/or accept your theory of evolution.Not sure this "exchange" will bear fruit... It is too one-sided. Pearls and swine and all that.
Had you considered that your admitted ignorance of the subject, coupled with your religious indoctrination, is at fault?It's not that, though I suppose from your end it could be seen that way toward me, lol. I just have not gotten from you anything but this one argument against something that more-knowledgeable-on-the-subject-than-I-am creationists argue. While you may be right and win that argument, you haven't convinced me of anything that I would need to reject creationism and/or accept your theory of evolution.
That is a start - isn't it interesting, then, that a few weeks ago, when you were 100% uninformed about basic genetics, you were supremely confident in your erroneous assertions on the subject? So much so that you would insult those that countered your assertions?From my point of view, you have only educated me a little, with something that appears intriguing. That's pretty much it.
I don't really know what you would expect. We get the same thing from supposed atheists about the existence of God —strawman arguments, false assumptions and simple turning away from what is as obvious (eg. first cause) as some of the things scientists pursue to prove.Thanks, @Mark Quayle . It is funny how creationists operate - all full of bombast and aggressive unwarranted confidence. Only to later tease out of them that they actually do not understand even the basics regarding what they are so confident about. Yes, so funny.
I don't really know what you would expect - there is no evidence or consensus for what God is, or its supposed properties, or the arguments for its existence. What you consider 'obvious' (e.g. first cause), many philosophers and physicists consider to be unjustified assertion, folk logic.I don't really know what you would expect. We get the same thing from supposed atheists about the existence of God —strawman arguments, false assumptions and simple turning away from what is as obvious (eg. first cause) as some of the things scientists pursue to prove.
Sure there is logic and consensus. First Cause. Omnipotence. And the many logically necessary attributes which follow: eg. benevolence, aseity, simplicity etc etc. The fact many deny it doesn't make it non-consensus as to the definition of God.I don't really know what you would expect - there is no evidence or consensus for what God is, or its supposed properties, or the arguments for its existence. What you consider 'obvious' (e.g. first cause), many philosophers and physicists consider to be unjustified assertion, folk logic.
Well, no. You may not be aware, but there are thousands of different gods with different attributes and properties.Sure there is logic and consensus. First Cause. Omnipotence. And the many logically necessary attributes which follow: eg. benevolence, aseity, simplicity etc etc. The fact many deny it doesn't make it non-consensus as to the definition of God.
As someone who writes code to study genetics for a living (my job title is 'senior computational scientist')... yeah. To the extent that genetics does resemble software, it resembles software that wasn't designed, that is riddled with redundancies, unused, dead code, patches to repair earlier bugs, and multiple modules doing similar things that look like they were written by different people.
Apples, meet oranges.I don't really know what you would expect. We get the same thing from supposed atheists about the existence of God —strawman arguments, false assumptions and simple turning away from what is as obvious (eg. first cause) as some of the things scientists pursue to prove.
But you just learned a couple of weeks ago about what mutations and gene duplications are!Anyhow, I still have not heard a strong enough set of data to show that there has been enough time to beneficially mutate reproducible generations from primordial soup to man.
I still have not been convinced that there are enough 'links' to fill enough of what's missing, for the theory to be convincing.
Oh, then you must have some actual evidence for Jehovah's existence (as well as the "other gods" mentioned in the 1st commandment).And most of all, I have not seen ANY indication that God did not do this just as Genesis lays it out.
Well sure - when you put magic being that can do anything it wants into the equation, how can you fail?Every objection I have heard laid out falls flat on its face when GOD is included in the equation.
A shame that @Torah Keeper never replied. I was looking forward to her explanations.Good, because it isn't.
Your awe is noted, but is totally subjective.
Perhaps because we do not rely on the fallacy of begging the question or the strawman fallacy and do not engage in the argument via awe?
Is it?
Please show the math that you employed in drawing that conclusion.
3 dimensional? Explain.
I see quite a bit of analogy and awe-based hyperbole there.
I am perplexed by much of it, but can you please explain the part I bolded, at least to start?
I see that you, too, do not understand what the phrase "genetic code" means. This is from a post I made on another forum on this subject:
For more detail, we can look at the page of the National Human Genome Research Institute - they would know, right?
The instructions in a gene that tell the cell how to make a specific protein. A, C, G, and T are the "letters" of the DNA code; they stand for the chemicals adenine (A), cytosine (C), guanine (G), and thymine (T), respectively, that make up the nucleotide bases of DNA. Each gene's code combines the four chemicals in various ways to spell out three-letter "words" that specify which amino acid is needed at every step in making a protein.
Bolding mine.
Not that hard, right? The illustration they use at the NHGRI:
That ^^^ is the genetic code.
And yet, we see creationists use it in very.... non-standard ways. To avoid being accused of 'call outs' and such, I will provide no links and use no names, but if you think I am being unfair or dishonest, you can always use the forum search tool.
A few examples:
"Although we do observe elements of adapation [sic] and natural selection in flipping the switches on already existing genetic codes - we never see the creation of new genetic code that would allow one kind of animal to turn into another kind."
"the genetic code drives the makeup of the body, not the mind.
there isn't a genetic code for consciousness"
"Does our genetic code change over the course of our lives?"
" The introduction of new functional genetic code information into an organism rather than merely toggling the switches of the genetic code that is already there."
"You still have not given any arguments to support your claim that any of the things you listed (polyploidy, horizontal gene transfer, plasmids, VNTRs, endogenous retroviruses,) could be used to explain how the new genetic code required for reptilian style scales could be introduced by random chance into a cat and result in replacing their fur."
"Adaptation is using the information already in the genetic codes to express changes in an organism.
Evolution is the introduction of new information, new code, that allows for doing something that the organisms previous genetic code did not have the ability to express through epigenetic adaptation."
Lots, lots more. But that is a nice sampling.
Seems like creationists conflate the actual "genetic code" with an organism's genes, or genome. Or something. This is among the many reasons it is hard to have real discussions with creationists - they conflate concepts/mis-define concepts/employ idiosyncratic definitions and expect others to use their fake ones/etc.
But hopefully they will learn,
In the end, there is really no need to 'read' the entire genome. So I am not sure what you think you are accomplishing with these factoids. Other than justifying your awe.
We know a LOT about it.
Bare assertions are cool, but pretty childish.
Truly, relying on such "arguments" may impress pew-warmers, but amongst educated adults, they just come off as pathetic.
But kudos for almost staying on topic!
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