Why do you think

Yeah, me too…I figured it was more in your face smugness…

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@skriten:

Ah, this takes us into the wonderful (but at times, sadly non-rigorous) world of epigenetics.

First we need a definition. Epigenetics covers the emergence of stable (and indeed, heritable) changes in an organism that do not arise from changes in a germline DNA sequence. So far, so good. But of course, the question naturally arises in the astute mind, what mechanisms underpin and facilitate said changes?.

Now on the Wikipedia page, the following factors are cited as being implicated in epigenetic change:

[1] Development (either in utero or during early childhood, or in corresponding stages in other organisms);
[2] Environmental chemicals;
[3] Pharmacoactive compounds;
[4] Aging;
[5] Diet.

However, there’s a little problem. While some well-understood mechanisms are proposed for some of these changes, others are, shall we say, left dangling in the wind a little. Furthermore, a deeper dive into some of the proposed mechanisms just cited, reveals that genetics is still underpinning said mechanisms.

Take development, for example, during which the selective silencing and activation of certain genes in certain embryonic cells, leads to the cells in question differentiating into various organs or tissues. A famous and tragic example of the disruption of this process is provided by Thalidomide, which in humans, results in gross interference with the operation of Hox genes (the genes responsible for the basic human bauplan), and generates the malformations that became a major public health scandal in the 1960s. However, I’m not aware of any literature that points to the resulting changes being heritable, and it should be obvious that questionable ethical boundaries would have to be crossed in order to determine this.

Furthermore, much of the literature on epigenetics covers, wait for it, DNA damage, which I would have thought, by definition, involved sequence changes.

One example that was presented to me some time ago as being ‘epigenetics’, was the differentiation of bee larval fates (referred to in the literature as "diphenic caste production), depending upon whether the larvae were fed “bee bread” (a mixture of pollen and other substances provided by worker adults) or “royal jelly” (a nutrient produced exclusively by queen bees). Rapamycin and FK506 pharmacology studies, along with RNAi knockdown, led to the discovery of a specific gene implicated in this process, which is selectively activated by the difference in diet. I’ll provide the relevant literature now, starting with:

The Making Of A Queen: TOR Pathway Is A Key Player In Diphenic Caste Development by Avani Patel, M. Kim Fondrk, Osman Kaftanoglu, Christine Emore, Greg Hunt, Katy Frederick, Gro V. Amdam, PLoS One, 6: e509 (June 2007), doi:10.1371/journal.pone.0000509

I quote from the paper thus:

What the authors did was to test the hypothesis that the kinase enzyme coded for by the TOR gene (in this case, the amTOR variant present in Apis mellifera) influenced development based upon environmental conditions.

Honey bee larvae are fed with a special substance known as ‘royal jelly’ for the first 48 hours of life. Those larvae destined to become workers (the majority) are then fed after this initial period with a food comprising pollen and other ingredients (nicknamed “bee bread”), and the amount of royal jelly that they receive is reduced significantly. A larva that is destined to become a queen, however, is fed royal jelly throughout its larval live in quantity. A special “queen cell” is constructed to receive the egg, the egg is laid therein, and the cell is stocked with a surplus of royal jelly (continually renewed so that the larva always has more royal jelly present than it can eat at one sitting).

Now, it turns out that the TOR pathway involves a nutrient sensitive kinase enzyme, and this has been found to be of influence in other insects in particular. That staple of genetics research, Drosophila melanogaster, was subject to TOR pathway investigation as cited by the above paper:

So, the authors considered it likely that the TOR pathway played at least some role in the differential development of bee larvae as described above.

So, how was this investigated?

Well, it turns out that the TOR enzyme, the nutrient sensitive kinase, is blocked by an antibiotic called rapamycin. Indeed, this property led to the TOR pathway being thus named - Target Of Rapamycin. So, one way of investigating whether or not the TOR pathway is involved in diphenic caste development is to feed queen-destined larvae with rapamycin, and see if the inhibition of the TOR pathway by rapamycin leads to worker characteristics in the adult insect. Which is exactly what happened when subject to experimental test.

However, the tests to implicate the TOR pathway in diphenic caste development were somewhat more sophisticated than mere rapamycin inhibition, as is described above. First, rapamycin inhibition is used to demonstrate that queen-destined larvae become workers when the TOR pathway is inhibited. Second, another antibiotic, FK506, competitively inhibits rapamycin, and leads to the restoration of the TOR pathway even in the presence of rapamycin. Therefore use of the two antibiotics can be used to provide a robust first-stage test of the connection between the TOR pathway and diphenic caste development.

So, having established that queen fate is associated with the TOR pathway, and that the kinase enzyme is somehow responsible for determining downstream signalling of other developmental aspects of a queen adult dependent upon royal jelly nutrient levels (details of this will doubtless be the subject of future papers), the next step was to establish that queen fate was due to elevated activity of the gene in question:

So, the scientists established that elevated expression of the gene was notable in queens, and that the signalling corresponded to the results from the pharmacology manipulation experiments.

As a second test, the scientists then used gene knockdown techniques to examine the effects of eliminating the expression of the gene altogether. To ensure that this was robust, another gene knockdown was used to ensure that the intended gene knockdown technique did not influence the TOR pathway as an artifact of using RNAi knockdown, but was specific to the gene in question.

So, what we have here is evidence that there is a genetic basis for phenotypic plasticity in Apis mellifera, leading to diphenic caste development depending upon the nutrient environment that the larva is reared in, and consequently evidence for the existence of at least one differential developmental process, based upon a specific gene, that can lead to two manifestly different outcomes in an organism on the basis of the effect of environmental influence upon that gene-driven developmental pathway. It is likely that similar interactions are going to be apposite in other developmental pathways (and in other organisms), and that it may transpire that epigenetic phenomena rest upon developmental pathways with built-in environmental cue sensitivity. Indeed, it was the investigation of the effect of the TOR pathway on Drosophila and other organisms in the first place that led to the investigation of the TOR pathway as a suitable control for diphenic caste development.

The above should prove informative with respect to some of the assertions surrounding epigenetics :slight_smile:

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Thanks for the response, and yes it is informative.

Edit (I’m not worthy :pensive:)

@WhoAreYou here, have fun.

And here is an in depth explanation why we know that Genesis story has one origin and it is not even from the first hand experience. It’s just a retold story.

Do you think that magic is real?

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Since @WhoAreYou has ignored my questions for many weeks now, I will be answering anything he posts, by repeating those questions:

So @WhoAreYou

  1. How does the human genome evidence a deity, as you claimed?
  2. Why is atheism almost universal among elite biologists, if as you claimed, there is evidence for a deity in their field of expertise?
  3. Why do you keep claiming the Noah myth has any validity, when the geological record demonstrates unequivocally no global flood has ever occurred? (see the video posted above by @AtheistChMG.

Since he has been relentlessly dishonest in evading these responses to his claims, these questions are all he will get from now on, until he makes some effort to offer a candid answer, that does not involve deflection or whataboutism, or outright evasion. Or an admission that he has no credible or rational answer, and some acknowledgement that these claims are not just unevidenced subjective beliefs he holds, but that they are actually falsified by objective evidence.

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@Sheldon:

Of course, another tactic to watch out for, is the one I refer to as “the creationist reboot”. This particular piece of duplicity arises, whenever a body of evidence refuting a creationist assertion is presented. What then happens is that [1] the creationist refuses even to acknowledge the existence of said presentation of refuting evidence, followed by [2] the creationist waiting until he/she thinks said presentation has been forgotten by the audience, followed by the resurrection of the previously refuted assertion as if it had never been addressed.

This tactic has been on display several times here already.

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Why are you attributing words to me that I have never spoken? You know, atheists can be just as intellectually dishonest as extremists of any religion.

No, my point is that a theory, even when tested with repeated evidence and appearing rational, may still be incorrect. This does not prove the existence of God. Rather, it demonstrates that human knowledge is more flawed and imaginative than we would prefer to acknowledge. That is the extent of it.

First and foremost, I want to emphasize that I am not a creationist. I want to make it clear, once again (and possibly for the fifth time), that my ideas about religion, mythology, or sentience are entirely separate from what I am currently discussing. This is merely an example highlighting how science can potentially believe in a mechanism that is flawed. The evidence lies in the fact that the simulation you provided is not generating the level of complexity that some of my simulations have achieved.

For instance, my simulations have successfully generated starfish, worms, fungi, spheres, and other naturally occurring organizational forms. What’s interesting is that this outcome was unexpected and emerged as a byproduct of employing a significantly different approach from yours.

Moreover, my simulations have been deliberately constrained to prevent excessive complexity that could overload the computer, produce an abundance of junk DNA, and occasionally duplicate the entire DNA sequence. They also demonstrate convergent evolution and neutral mutations that contribute to it. In fact, these simulations exhibit many of the phenomena observed in nature. On the other hand, your simulation is incapable of producing even a fraction of these results.

And NO… I’M NOT A GENIUS. I’m just an ordinary person who asked the right question.

Therefore, it is important to acknowledge that your model of evolution is incapable of producing the anticipated outcome when simulated.

In short, the organism has the ability to control the mutation rates in different sections of the genetic code. This opens the door to a wide range of consequences that can essentially be summarized as “mutations are not entirely random.”

This is a perfect example of censorship in science being used to sustain a fundamentally flawed mechanism. I kindly request that you conduct a simulation yourself to demonstrate your understanding of the functionality of evolution.

Thank you.

Liar, you claimed that evolution was incompatible with an atheistic worldview. You also claimed that core aspects of evolution were wrong, and that you knew better than “99%” of biologists, and were going to prove this, nothing on the news yet of course, quelle surprise.

So a straw man that no one has ever disputed. However this is also mendacious, since you claimed evolution is incorrect, and you claimed to know this, and claimed “99%” of biologists were wrong, and that you would prove it. So using the phrase “may still be incorrect” is doubly dishonest here. Why you think you can lie to us with impunity like this isn’t clear, but all anyone need do is read through your posts.

Gerraway…

Science and its methods are demonstrably more successful at understanding reality than the kind of unevidenced superstition you’re peddling. In fact science is demonstrably our best method by any objective margin.

No it wasn’t, you’re lying again.

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So, YOu are admitting you are wrong?

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Hmmm :face_with_raised_eyebrow: I guess I still have to write here to post. (Flawed stupid forum techies :man_technologist:)

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Essentially Quin is correct; however, he is attempting to reduce ‘theory’ to something akin to ‘common knowledge.’ Even when theories are incorrect, they rarely lose their utility. Euclidian Geometry and Non-Euclidian Geometry, Newtonian Gravity and Einstein Gravity, for examples. Any new theory must do a better job of explaining all the facts than the old theory. It is not that the theory is wrong, it is that we have found a new way to organize the facts. A way to see them differently and more encompassing. A theory is the height of scientific understanding. It is the very best we can do with our current knowledge. It is what is accepted by the best and brightest on our planet. Quin’s ‘poo-poo’ of the idea of scientific theory is not worth the page it is written on. The idea that ‘Theories change,’ or may be incorrect, is built on pure ignorance of the scientific method.

What are your degrees in Quin?

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For sure. Theories really aren’t right or wrong; they are like tools; they are useful (or not so useful). I would also like to mention that geometry isn’t a theory.

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I have explained to you at least three times what I truly meant with this phrase. It was never my intention to imply that evolution proves the existence of God. Rather, I was trying to convey that evolution appears to favor theistic human groups over atheistic groups. This is what I genuinely meant, and it seems that you are unwilling to accept this, persistently believing that by doing so, you will have a valid point.

This is absurd. It is illogical to engage in a conversation with someone who keeps asking the same question, despite my explicit statement that the meaning you are inquiring about is NOT the meaning I intended to communicate.

Well, the scientific method is susceptible to manipulation by economic and political interests. Pharmaceutical research is a well-known example of this, and it is not a conspiracy theory. A quick search can verify what I am saying.

Of course, science is and has always been influenced by the economic and political dynamics of the time. When religion was predominant, “all evidence” seemed to confirm the existence of God. And now, with capitalism prevailing, “all evidence” seems to deny the existence of God.

It is evident that the academic world is rife with prejudices, interests, subjectivity, power struggles, individuals who have lost touch with reality, and those who vehemently defend their theses without considering anything beyond them. Additionally, there are those who are compelled to publish in order to sustain themselves.

While it is true that academia is the best system we currently have, it still has room for improvement.

Oh, please do share your publications and the journals in which your articles appear.

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I’d be interested in the rejected ones :smirk:

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No.

People can be manipulated.

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How handy! Changing the meaning of what one has said is such a useful tool when one is caught with one’s pants down.

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What in the wide, wide world of sports does capitalism have to do with theism?
And are you intimating that these two things are mutually exclusive?

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