Bee genome changes dramatically through life

_{Denyse O'Leary

September 13, 2018

Epigenetics, Genetics

1}_{Categories
Epigenetics
Genetics}

Share: Facebook; Twitter/X; LinkedIn; Flipboard; Print; Email

Pollinating Bee Remember old-fashioned, unalterable DNA? It was interesting stuff. So now this:

“A study of chemical tags on histone proteins hints at how the same genome can yield very different animals:”

The bee genome has a superpower. Not only can the exact same DNA sequence yield three types of insect—worker, drone, and queen—that look and behave very differently, but, in the case of workers, it dictates different sets of behaviors.

A key to the genome’s versatility seems to be epigenetic changes—chemical tags that, when added or removed from DNA, change the activity of a gene. Previous studies had shown distinct patterns of tags known as methyl groups on the genomes of bees performing different roles within their hives.Shawna Williams, “As Bees Specialize, So Does Their DNA Packaging” at The Scientist

One wonders what the tax-funded textbooks are still saying about DNA…

See also: Evolution is evolving? [It had better be.] The conference seems to be dedicated to the extended evolutionary synthesis, which it contrasts with the “modern synthesis”

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

Comments

jawa, Don’t you have more important things to occupy your time in? Please, don’t take me wrong, but I think you should get help from counseling. I really feel sad for you. Nobody is obligated to respond or comment on other comments here. You have to understand that.PeterA_{October 1, 2018
October
10
Oct
1
01
2018
07:56 AM
7
07
56
AM
PDT}

RJ Sawyer, I’m glad to know that Peter and you won’t lose any sleep. Sleep deprivation may be detrimental to health. However, I just want to call the anonymous readers’ attention to the fact that some commenters quit discussing unexpectedly and it seems like sometimes that has to do with lacking strong arguments against the other side, though perhaps that’s not really the reason for their apathy. Apparently the comment @197 has been ignored by the person to whom it was addressed to. But the author has ignored some comments too. That’s all. Y’all may keep sleeping. But don’t sleep in the subway.* (*) 1967 Petula Clark :)jawa_{September 30, 2018
September
09
Sep
30
30
2018
04:12 PM
4
04
12
PM
PDT}

Jawa@198&199, your obsession with the amount of time people attend to your demands, or ignore them, is duly noted. But I don’t think that Peter or I will lose any sleep over your concerns.R J Sawyer_{September 25, 2018
September
09
Sep
25
25
2018
01:53 PM
1
01
53
PM
PDT}

Peter, Bad news for you. RJ Sawyer has openly ignored your comment. He’s not interested in discussing biology. Apparently more interested in philosophical arguments, as you can see in other discussions. I’m glad you’ve been given your own bitter medicine back. Good for you. Perhaps that will teach you a lesson. Now you know how rude it’s to quit a conversation without any explanation. You did it to me.jawa_{September 25, 2018
September
09
Sep
25
25
2018
12:17 PM
12
12
17
PM
PDT}

Peter, Your inconsistency has increased almost to the pathetic level of Amblyrhynchus. You apologize to TJ Sawyer for leaving him waiting 2 days for your response. However, it has been 4 days since you ignored my questions addressed to you @152, which were reminded @165. Can you explain?jawa_{September 24, 2018
September
09
Sep
24
24
2018
06:59 AM
6
06
59
AM
PDT}

RJ Sawyer @175: I apologize for leaving you waiting for a couple of days. I was busy working on important tasks. Please, don’t give up so easily. I’m sure you know that famous document. It’s from the second half of the 19th century England. Its famous author proposed a then revolutionary idea based on observations of evolutionary adaptations (micro-evolution) but made the enormous mistake of extrapolating those observations up to the level of baramins! Attributed extraordinary powers to the allegedly micro-evolutionary RV+NS and incorrectly proposed that such limited mechanisms could eventually lead to the baramins! It took many years for some scientists to wake up from the dumbing effect of such mistaken extrapolation, but fortunately now some scientists even within the materialistic worldview have admitted that the failed extrapolation requires serious revision. They have jumped out of the ship where they sailed for long time and have boarded their own “third way” ship. Some have dared to ask for a complete replacement, but others more cautious have reacted like John Lennon in his song “Revolution”, agreeing with changes while opposing destruction. The peaceful folks have proposed an extension to the original ideas to account for the major gaps in the original RV+NS path. I’m sure now you realize what famous document this is about.PeterA_{September 22, 2018
September
09
Sep
22
22
2018
01:43 PM
1
01
43
PM
PDT}

GP "I agree with you." Great! "Abel has everything perfectly right." I like this author. To be a bit critical and hair-splitting, I would not call what he writes about "the birth of programming" (his own words) but... what he writes and how sets the teeth of the likes of Jeffrey Shallit on edge :)EugeneS_{September 22, 2018
September
09
Sep
22
22
2018
10:29 AM
10
10
29
AM
PDT}

DATCG: About intrinsically disordered regions in TFs, I have just posted a link to a paper, at comment #287 in the transcription regulation thread. :)gpuccio_{September 22, 2018
September
09
Sep
22
22
2018
08:45 AM
8
08
45
AM
PDT}

DATCG: Abel has everything perfectly right. I would just add that, while folding is certainly a big part of functional specification, there are however a lot of other sequence specificities that are not necessarily related to classical folding. Of course there are active sites that are as important as the general 3D folding, but as we know well there are also many sequences, not corresponding to well folded domains, that have great functional importance: they go, in general, under the name of intrinsically disordered proteins or intrinsically disordered regions, but many different functional mechanisms can be hidden behind that concept.gpuccio_{September 22, 2018
September
09
Sep
22
22
2018
07:47 AM
7
07
47
AM
PDT}

EugeneS> I agree with you. Animals can certainly learn.gpuccio_{September 22, 2018
September
09
Sep
22
22
2018
07:40 AM
7
07
40
AM
PDT}

GP I can agree with almost everything you said in your previous comment. I guess when I said that animals program themselves I was too vague. All of this comment is just thinking aloud... I do not believe that all instincts are written in stone and have been necessarily front loaded. I think that at least some animals can genuinely learn (work out strategies and correct them based on previous experiences). Of course, these abilities in animals are inferior to their human counterparts.EugeneS_{September 22, 2018
September
09
Sep
22
22
2018
06:49 AM
6
06
49
AM
PDT}

DATCG, Very interesting comments @189, 190. Thanks.OLV_{September 22, 2018
September
09
Sep
22
22
2018
01:11 AM
1
01
11
AM
PDT}

Functional Sequence Complexity(FSC)
Bioinformation has been selected algorithmically at the covalently-bound sequence level to instruct eventual three-dimensional shape. The shape is specific for a certain structural, catalytic, or regulatory function. All of these functions must be integrated into a symphony of metabolic functions. Apart from actually producing function, "information" has little or no value. What kind of information produces function? In computer science, we call it a "program." A linear, digital, cybernetic string of symbols representing syntactic, semantic and pragmatic prescription; each successive sign in the string is a representation of a decision-node configurable switch-setting – a specific selection for function. FSC is a succession of algorithmic selections leading to function. Selection, specification, or signification of certain "choices" in FSC sequences results only from nonrandom selection. These selections at successive decision nodes cannot be forced by deterministic cause-and-effect necessity. If they were, nearly all decision-node selections would be the same. They would be highly ordered (OSC)(Edit - Like Snow, Ice. And the selections cannot be random (RSC). No sophisticated program has ever been observed to be written by successive coin flips where heads is "1" and tails is "0." Shannon [2,3] was interested in signal space, not in particular messages. Shannon mathematics deals only with averaged probabilistic combinatorics. FSC requires a specification of the sequence of FSC choices. They cannot be averaged without loss of Prescriptive Information (instructions). Bits in a computer program measure only the number of binary choice opportunities. Bits do not measure or indicate which specific choices are made. Enumerating the specific choices that work is the very essence of gaining information (in the intuitive sense). When we buy a computer program, we are paying for sequences of integrated specific decision-node choice-commitments that we expect to work for us. The essence of the instruction is the enumeration of the sequence of particular choices. This necessity defines the very goal of genome projects. Algorithms are processes or procedures that produce a needed result, whether it is computation or the end-products of biochemical pathways. Such strings of decision-node selections are anything but random. And they are not "self-ordered" by redundant cause-and-effect necessity. Every successive nucleotide is a quaternary "switch setting." Many nucleotide selections in the string are not critical. But those switch-settings that determine folding, especially, are highly "meaningful." Functional switch-setting sequences are produced only by uncoerced selection pressure. There is a cybernetic aspect of life processes that is directly analogous to that of computer programming. More attention should be focused on the reality and mechanisms of selection at the decision-node level of biological algorithms.
Codes of Life, not blind, but guided, not simply ordered, but symbolic, highly organized, functional sequences that have purpose and targets to repair, protect and regenerate trillions of times in our cells each day not blindly, but programmatic steps and instructions, rules and conditions. What a marvelous work it is this Code of Life, that ENCODE projects are unraveling evermore these days. .DATCG_{September 21, 2018
September
09
Sep
21
21
2018
09:41 PM
9
09
41
PM
PDT}

Gpuccio @176, Well done in reference to Abel, Order vs Functional. Configurable Switches. I think RJ Sawyer is not recognizing differences between Ordered Sequence Complexity(OSC) - snow, ice, and Functional Sequence Complexity(FSC) - symbolic representation and abstract messaging for a myriad of specified forms. Pre-Programmed and prescribed informational content. From Trevor and Abel's paper... Ordered Sequence Complexity (OSC)
A linear string of linked units, the sequencing of which is patterned either by the natural regularities described by physical laws (necessity) or by statistically weighted means (e.g., unequal availability of units), but which is not patterned by deliberate choice contingency (agency). Ordered Sequence Complexity is exampled by a dotted line and by polymers such as polysaccharides. OSC in nature is so ruled by redundant cause-and-effect "necessity" that it affords the least complexity of the three types of sequences.(edit: example - ice). The mantra-like matrix of OSC has little capacity to retain information. OSC would limit so severely information retention that the sequence could not direct the simplest of biochemical pathways, let alone integrated metabolism. Appealing to "unknown laws" as life-origin explanations is nothing more than an appeal to cause-and-effect necessity. The latter only produces OSC with greater order, less complexity, and less potential for eventual information retention (Figs. ?(Figs.11 and ? and 22).
Another words, liquid water, rain to snow and ice does not create artistic images of design like those at following link on ice sculptures... https://www.complex.com/style/2011/12/the-25-most-spectacular-snow-sculptures/3 Funny, the site name is "complex.com" ;-) .DATCG_{September 21, 2018
September
09
Sep
21
21
2018
09:31 PM
9
09
31
PM
PDT}

I see we are not going to hear what information is in a molecule of water. Likewise, we are not going to hear if the confirmed prediction of a semantically closed, multi-referent symbol system at the heart of the cell (a language structure, as carefully described in the physics literature) is an inference to an act of intelligence or an unguided dynamic process. Too bad.Upright BiPed_{September 21, 2018
September
09
Sep
21
21
2018
06:38 PM
6
06
38
PM
PDT}

The word “intelligo”, after all, means just that: I understand. If an “AI” robot can be programmed to say “I understand” would it have the same meaning as one of us saying it? Who is “I” in each case? A conscious or non-conscious being? Isn’t there a big difference in lacking or having consciousness? On another, though related topic, are the cats self aware of their own existence? We would have to ask them. :) Also, how does it feel to be a cat? Let’s ask them too. :)OLV_{September 21, 2018
September
09
Sep
21
21
2018
02:56 PM
2
02
56
PM
PDT}

EugeneS: If we create AI (which is not conscious), we do it consciously. AI requires complex functional information to work. And it's our conscious representations that allow us to generate the complex functional information that works as AI. Animals are conscious, IMO, at least higher animals certainly are. But I don't see how they could "program themselves", either consciously or not. To "program" means to use highly symbolic intelligence to achieve a goal by complex functional configurations. Animals apparently cannot do that. What they can do is to use their conscious representations to find solutions and procedures that are not highly symbolic, but are still intelligent: like my cat opening the door. How is that done? Again, there is a conscious representation of feeling, a desire. My cat wants the door open. Then there are cognitive representations of meaning: what possible actions can open the door. Not highly symbolic cognition, but cognition just the same. And there is coordinated action and cognition: attempts, evaluation of results. And, in the end, success. Nothing of that could happen without conscious representations, I believe. However, something is still missing: higher symbolic language, higher abstraction, and so on. I don't think an animal can "program". It can learn, and it does that by conscious representations of feeling and cognition, like us. Just simpler. An animal cannot create AI. Indeed, they cannot create even simpler machines, with few minimal exceptions. They usually cannot create complex symbolic language. Again, with some partial exceptions. Those behaviours that are very complex and instinctive, and for which we have no evidence that they are the result of individual learning, are reasonably pre-programmed. And they cannot be pre-programmed by the animal itself. I don'think that monarch butterflies have learnt how to migrate. Or beavers how to build dams. Regarding AI, I would say that it is an intelligently designed machine. In that sense, it is not different from a watch, just more complex. Is a watch intelligent? Or an abacus? Or a computer? All of them are, in a sense. They are intelligently designed machines. None of them is, in another sense. None of those objects can have any conscious cognition, any understanding of meaning, any desire. And those are the things that really define intelligence. The word "intelligo", after all, means just that: I understand.gpuccio_{September 21, 2018
September
09
Sep
21
21
2018
01:56 PM
1
01
56
PM
PDT}

GP and all ;) Sorry for the typos. Fishy fingers on a London train.EugeneS_{September 21, 2018
September
09
Sep
21
21
2018
10:49 AM
10
10
49
AM
PDT}

GP Conscious representations. I can see where you are coming from. Yes, I agree, a lit of those behaviours are instinctive and may have been preprogrammed. But surely it is possible for animals to program themselves, consciously or not. The latter would be IMO equivalenttous creating AI. AI is intelligence in its own right by many criteria (except being conscious)...EugeneS_{September 21, 2018
September
09
Sep
21
21
2018
10:35 AM
10
10
35
AM
PDT}

EugeneS at #180: That is an old an interesting point. My point of view is as follows. I believe that some animals can generate forms of functional complexity in their individual behaviours. One of my cats, for example, can jump and open doors by grasping the handle. My two other cats cannot do that at all. In general, these forms of intelligent behaviour are probably of lower complexity than what we can see in humans, and rarely they reach higher abstraction levels, especially symbolic codes. But of course that is a very interesting field of research. Beaver dams and similar examples, however, are probably different from that. I think we are in the field of this OP with those examples: complex and intelligent instinctive behaviour. The difference here is that those behaviours are, in great part, hereditary. They are repeated in the species. They are not like my cat opening doors, but rather like my cat purring or licking itself. Be they genetic or epigenetic, they seem to be hereditary. Therefore, the information that governs those behaviours is probably in the genome, or maybe in the epigenome, or in both. IOWs, there is a very good chance that such information is designed, exactly like all other biological information. In that case, the designer of that information would not be the indvidual animal (like in the case of my cat opening doors), but rather the biological designer of the species. In the end, however, human design remains the best, if not the only, example of conscious design generating high functional complexity. Even if we consider animals capable of that too, in some measure, that ability would again rely on conscious representations (I have no doubts that my cat learned to open the doors because it wanted to do that, and in some way it understood how to do it). However, in humans we have a direct window to the connection between conscious representations and design: our own personal consciousness, which allows us to have direct experience of the conscious representations that precede and cause the act of design in ourselves. And to infer the same thing, with the highest reliability, for other humans.gpuccio_{September 21, 2018
September
09
Sep
21
21
2018
07:42 AM
7
07
42
AM
PDT}

EugeneS @180: That’s an interesting point with a persuading argument. Thanks.PaoloV_{September 21, 2018
September
09
Sep
21
21
2018
05:36 AM
5
05
36
AM
PDT}

Yes, i agree that gpuccio wrote another insightful explanation, but we’re all used to this here. The guy has set the bar so high that his friendly opponents can’t even see it. It almost looks unfair according to the “politically correct” rules of this world.jawa_{September 21, 2018
September
09
Sep
21
21
2018
05:28 AM
5
05
28
AM
PDT}

GP 176, An excellent comment. The only thing that requires further clarification/research IMO is whether human artefacts are indeed a single class of such objects. While animal contraptions, for want of a better word, such as beaver dams and termite hills and bird nests are certainly less complex than the most complex human artefacts, in terms of concrete thteshold values for ID detection they may still qualify.EugeneS_{September 21, 2018
September
09
Sep
21
21
2018
05:20 AM
5
05
20
AM
PDT}

PeterA, After I addressed new questions to you @165, you continued your friendly chat with RJ Sawyer in this thread and wrote comments @168 and @173 for him, but ignored me. Any reason that justifies your attitude?jawa_{September 21, 2018
September
09
Sep
21
21
2018
05:16 AM
5
05
16
AM
PDT}

@176 “There is absolutely no scientific evidence for that strange imaginary theory, except for the blind faith of those who need to believe in it out of a personal commitment to a materialistic worldview in science. And personal commitments have no relevance in true science.” Excellent conclusion to his excellent explanation.PaoloV_{September 21, 2018
September
09
Sep
21
21
2018
05:02 AM
5
05
02
AM
PDT}

I can’t tell exactly why, but I like to read gpuccio’s comments on the topic that is discussed here. There’s always some learning from it. I’m sure DATCG, UB and other folks here enjoy it too.OLV_{September 21, 2018
September
09
Sep
21
21
2018
03:37 AM
3
03
37
AM
PDT}

R J Sawyer at #160: Thank you for your thoughts. You make two "objections" in your comment, and I would like to answer them both, as they are common objections to ID theory and they deserve a clear answer. If I understand well, they are (in a logical order, not in the order you gave them in the comment): 1) "I have difficulties with trying to figure out what is meant by “complex functional specified information”. And the water molecule example. 2) "My problem with the “complex functional specified information is solely the product of conscious design “ argument is that we are drawing this conclusion from a single example, human. It is always dangerous to extrapolate from a single example." OK, let's go with it. 1) We can argue about possible functions of water, and as you know I am open to all possible definitions of function in my approach to functional complexity. But that is not the problem. The problem with water is not the function, but the complexity linked to it. Let's try to clarify. The complexity in "functional complexity" is not a generic notion of complexity: it is very specific and well defined. The complexity is the ratio of the configurations of the observed object that implement the function versus all possible configurations of the object. And the important point is: those configurations must be similarly possible under the laws of physics. IOWs, functional complexity refers to specific configurations of what Abel calls "configurable switches", configurations that implement a function, while all the other possible configurations do not implement it. The ratio of the target space to the search space is the functional complexity observed in the object, for the defined function. Now, the key point, again, is that all the configurations in the search space must be possible under the laws of physics. IOWs, a configurable switch is something that, under physical laws, can assume different configurations (at least two) that are possible under physical laws: IOWs, contingent configurations. So, in a nucleic acid each of the four nucleotides can be found at some place, in the absence of some template which already has the information. There is no law of physicis or biochemistry that dictates that, for example, the first nucleotide must be A, the second T, the third A, the fourth G, and so on. IOWs, there are no laws of physicis of chemistry that dictate a specific sequence, in the absence of any template that already has that information. The same is true for AAs in a protein. Can necessity dictate a sequence in particular cases? Of course it can. Let's say that in your medium in your lab you only have glycine available. Then you will only have polyglycines. But that is not a complex result: it is the result of necessity, an order easily compressible and easily explainable by the laws of chemistry, considering that only one aminoacid was available. Its Kolmogorov complexity is extremely low. So, even if the polyglycine could have some function (it certainly can), it is not complex. But consider insulin. In humans, it is a specific 110 AAs sequence, with a well definable function. Of course, there are many possible sequences that can implement the function of insulin, but their number is however reasonably small if compared to the 20^110 combinations that make the search space. If we can reasonable estimate the target space, then the functional complexity can be computed. However, there can be no doubt that there is a remarkable functional complexity here, and that it is of some relevance. My procedure of blasting the human form against cartilaginous fish gives an estimate of 97.8 bits, 49% identities, 0.889 baas: not much, if compared to other proteins, but still we have almost 100 bits of functional information here. Compare that to histone H3, a protein of similar length (136 AAs), which, with the same procedure, gives a result of 272 bits, 99% identities and 2.0 baas. Now, what about water? The answer is simple enough. If we accept the laws of physics and chemistry as they are, and the conditions of our planet as they are, the existence and configuration of the water molecule is completely explained by necessity: IOWs, water is like the polyglycin, not like the insulin molecule. So, from the point of view of functional complexity, it is not complex at all. No configurable switches show a specific configuration against possible configurations, simply because no other possible configurations exist. Can we make an argument for design about water? Yes, we can. But it must be either: a) The argument that the laws of our universe are designed (IOWs, a cosmological argument) b) The argument that some specific context in our universe is designed: for example, our planet (IOWs, a privileged planet argument) Both arguments are possible and, IMO, valid. But they have nothing to do with the configuration of water itself. They have to do with the configuration of our universe vs all possible universes, or with the configuration of our planet vs all possible planets. IOWs, the object we are observing in a) is the whole universe, and the object we are observing in b) is our planet. But if the object we are observing is water, no argument for design based on functional complexity can be made. I hope that is clear. 2) It is true that we are drawing our design inference for biological objects from a single class of observed objects, human artifacts. Not really one example, but certainly one class of examples. It's the observation of human artifacts that reveals to us the connection between functional complexity and conscious design. But the simple truth is: we are not deriving our theory about functional complexity and design from one class of objects because we want to be unduly selective. The reason is completely different. The reason is simply that human artifacts are the only class of objects in the universe, whose origin is not controversial, that exhibits complex functional information. In the whole universe as we know it. IOWs, there are only three classes of objects in the universe as we know it that have a specific status about functional complexity: a) Human artifacts, that exhibit tons of it. b) Biological objects, that exhibit tons of it. c) All other objects in the universe, that exhibit no functional complexity at all, beyond some very trivial level: IOWs, no complex functional information. So, if we accept the very simple notion that biological objects cannot easily be explained by natural laws (as everyone should see), and so we accept the simple notion that their origin is controversial (as the same existence of our debate should easily prove), then our choice of human artifacts as the only reliable source of information about functional information, design and their relationship becomes the only possible choice. IOWs, it's not the fact that we draw our conclusions from the class of human arrtifacts that is important: the important thing is that no other class of physical objects exists, in the whole universe, to draw conclusions about functional complexity, because no such class exists that exhibits complex functional complexity. Now, if there were a reliable explanation of how biological objects arise out of physical laws, then things would be different. IOWs, if the RV + NS alogrithm were capable of generating complex functional information, that would falsify ID. As I have always said. But the simple fact is that it is not capable of that. There is absolutely no scientific evidence for that strange imaginary theory, except for the blind faith of those who need to believe in it out of a personal commitment to a materialistic worldview in science. And personal commitments have no relevance in true science.gpuccio_{September 20, 2018
September
09
Sep
20
20
2018
11:42 PM
11
11
42
PM
PDT}

PeterA
However, I was interested in another case that is written in famous documents. Can you recall it?
The literature is full of examples of extrapolations, correlations and inferences being shown to be wrong. But obviously you have a famous one in mind. Don’t leave me hanging.R J Sawyer_{September 20, 2018
September
09
Sep
20
20
2018
04:30 PM
4
04
30
PM
PDT}

For example, can a water molecule
Can you explain what information does a water molecule contain? And would you mind addressing the question I asked you 135 comments ago at #38?Upright BiPed_{September 20, 2018
September
09
Sep
20
20
2018
04:01 PM
4
04
01
PM
PDT}

Archbishop Usher? Huh? Don’t recall ever hearing that name. I’m replying to you before searching for that name. However, my cultural/educational level is rather poor by all standards, so don’t take it as a pattern for comparison. In any case, it’s not the Christian Bible, hence it doesn’t count in this case. Many things have been said and even written by many people through history, but at the end of the day most of it doesn’t count, because it’s not a faithful interpretation of what is written in the Christian Scriptures. We humans like to make a text say less or more than what it really says, and when we don’t understand exactly what it says, then rather than humbly accept our poor comprehension, we prefer to speculate and make things up. However, leaving the momentary digression into obscure history and philosophy/theology, let’s go back to our science-related conversation. Please, would you mind commenting on the second part of #168? Thanks.PeterA_{September 20, 2018
September
09
Sep
20
20
2018
03:55 PM
3
03
55
PM
PDT}

1 2 3 … 7 Next

You must be logged in to post a comment.

Leave a Reply