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Author Topic:   Paper Discussion: Epigenesis and Complexity: The Coming Revolution in Biology
mobioevo
Member (Idle past 4844 days)
Posts: 34
From: Texas
Joined: 12-13-2007


Message 1 of 12 (441461)
12-17-2007 7:14 PM


I would like to discuss the following paper paper by Richard C. Strohman. While I believe Dr. Strohman is nutty, he gives an interesting discussion in this paper. Briefly summarizing, he says there is a coming revolution in biological understanding of the cell and that genetic determinism does not adequately support the complexity of the genome. He gives epigenetic phenomenon as an example that may be of influence.

Dr. Strohman retired in 1991 and this paper was published in 1997 and is very out of date. Much of the paper is over the philosophy of science rather than of actual research and explanations conducted, but none the less, if you are able to skip the philosophical pseudoscience you may find it a great paper for an intro to epigenetic studies.

Definition & Examples

The author is speaking about epigenetics. Epigenetics is the study of reversible, heritable changes in gene regulation that do not change the genotype. Epigenetics is a type of non-Mendelian inheritance, which is defined as heritable traits that segregate differently than defined in Mendel's laws.

I wrote about an example of an epigenetic phenomenon here, but there are many examples in the wikipedia entry for epigenetics.

This is what brought me to this paper. I feel it brings up a good topic in biology.

quote:
If genes don't determine us then what does? The answers that "The environment determines....", or that "Genes together with environment determine complex behavior" are really no help in biology because with either of these we are still left with the cell or organism as a neutral space in which random events somehow work out adaptive responses to changing conditions. I shall try to show that our major trouble... is that we have no theory of the cell or organism which explains how either of these manages to constrain or collapse an enormously complex realm of possibility to a given adaptive reality.

Some of the evidence the author uses against genetic determinism is:

quote:
Humans and mice have the same number of expressed genes (exclusive of socalled junk DNA) and yet they are radically different creatures. Older findings have revealed the similarity (98%+) between human and chimpanzee DNA and yet these two organisms manage to construct very different results from their nearly identical genes..."sibling species" show us organisms that appear to be identical under the most stringent anatomical observation and yet are found to be entirely different when examined at the level of their genes and of their proteins. These organisms offer the reverse of the human-chimp problem since they extract from extremely different genomes identical phenotypic end points.

The authors main point in the paper is,

quote:
...we have wrongly extended the theory of the gene to another area altogether; we have been lulled into reasoning that if the gene theory works at one level ... from DNA to protein ... it must work at all higher levels as well [for example epigenetics].

The purpose of this discussion is to get other ideas on if you think this author is correct in the above and other statements he makes in the paper. In my opinion, which I alluded to earlier, I think he is wrong which I will try to show in the future. What do you think the impact epigenetics will have on genetic determinism and evolution?

Edited by mobioevo, : spelling

Edited by mobioevo, : definition

Edited by mobioevo, : added quotes and some more questions.

Edited by mobioevo, : No reason given.


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 Message 11 by MartinV, posted 12-21-2007 11:53 AM mobioevo has not yet responded

  
Adminnemooseus
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Message 2 of 12 (441831)
12-18-2007 9:26 PM
Reply to: Message 1 by mobioevo
12-17-2007 7:14 PM


Pre-promotion note(s)
I think it would have been nice had there been some relevant quotes from the paper included in message 1. Perhaps members can supply such in the upcoming messages?

Stand by for topic promotion.

Any replies to this message should go to the "Considerations of topic promotions..." topic, link below.

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This message is a reply to:
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Adminnemooseus
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Message 3 of 12 (441834)
12-18-2007 9:26 PM


Thread moved here from the Proposed New Topics forum.

  
RAZD
Member (Idle past 304 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 4 of 12 (441839)
12-18-2007 10:04 PM
Reply to: Message 1 by mobioevo
12-17-2007 7:14 PM


I agree with moose that -- if you want to discuss the paper -- quotes pertinent to the issues you want to discuss will help focus the discussion, like:

quote:
Conflicts within genetic determinism

Genetic determinism is in trouble for the following reasons. Anomalous findings, the first signs of a Kuhnian revolt, are showing up almost weekly in major journals of molecular and cell biology. Among the disturbing findings coming from the Human Genome Project and elsewhere are:

(i) That genome complexity found in humans and mice, for example, is not correlated with the differences of form and function found between them3. ... Most biologists, when pushed, do agree that there is not enough information in any genome capable of mapping out the details by which morphological structures arise in organisms4.

(ii) there is a striking lack of correspondence between genetic and evolutionary change. Neo-Darwinian theory predicts a steady, slow continuous accumulation of mutations (micro evolution) that produces a progresisve change in morphology leading to new species, genera, and so on (macro evolution). But macro evolution now appears to be full of discontinuities (punctuated evolution) so we have a mismatch of some importance.


If you just want to discuss epigenesis, then perhaps some oppositional papers might help.

http://en.wikipedia.org/wiki/Epigenesis_%28biology%29

quote:
In biology, epigenesis has at least two distinct meanings:

  • the unfolding development of an organism, and in particular the development of a plant or animal from an egg or spore through a sequence of steps in which cells differentiate and organs form;

  • the theory that plants and animals develop in this way, in contrast to theories of preformation.

    ... Although both traditions tried to explain developmental organization, religious and metaphysical arguments on the conception of embryonic matter as either active or passive determined the scope of their respective explanations. ...


  • Sounds a little like Elmer and IamJoseph.

    Are we getting into evo/devo or staying more narrowly focussed?

    Thanks.

    Edited by RAZD, : added (ii)


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    This message is a reply to:
     Message 1 by mobioevo, posted 12-17-2007 7:14 PM mobioevo has responded

    Replies to this message:
     Message 5 by mobioevo, posted 12-18-2007 10:50 PM RAZD has responded

      
    mobioevo
    Member (Idle past 4844 days)
    Posts: 34
    From: Texas
    Joined: 12-13-2007


    Message 5 of 12 (441846)
    12-18-2007 10:50 PM
    Reply to: Message 4 by RAZD
    12-18-2007 10:04 PM


    I didn't add any quotes from the paper because I wanted others to read the paper and not just the quotes that I would write. You are probably right so I will do so in my next posts. Right now I wanted to define some of what the paper is concerned.

    The author is speaking more about epigenetics instead of the epigenesis that RAZD quoted from wikipedia. Epigenetics is the study of reversible, heritable changes in gene regulation that do not change the genotype.

    I wrote about an example of an epigenetic phenomenon here, but there are many examples in the wikipedia entry for epigenetics. Evodevo has a lot to do with this topic and I will speak more of it later.

    The author's argument for the paper being discussed is since there is more evidence that their are other forms of non-genetic inheritance will genetic determinism still survive. In the author's opinion no. He feels a more fully theory of the cell will develop out of epigenetic phenomenon.

    My answers to the authors critique of genetic determinism is, so what. Evolution needs to act on hereditary information. Whether this hereditary information is genetic, protein, RNA, methylation patterns, or cell membranes, it does not change the fact that they all are hereditary. A knowledge of epigenetic phenomenon only confirms that what is the hereditary unit is the ultimate source of selection. Over the next few days I will pick at the paper and follow with commentary of my own. I hope that others join me and add their opinion to my own.


    This message is a reply to:
     Message 4 by RAZD, posted 12-18-2007 10:04 PM RAZD has responded

    Replies to this message:
     Message 6 by Elmer, posted 12-19-2007 8:23 AM mobioevo has not yet responded
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     Message 12 by miosim, posted 01-05-2008 3:58 PM mobioevo has not yet responded

      
    Elmer
    Member (Idle past 4803 days)
    Posts: 82
    Joined: 01-15-2007


    Message 6 of 12 (441892)
    12-19-2007 8:23 AM
    Reply to: Message 5 by mobioevo
    12-18-2007 10:50 PM


    Hi mobioevo;

    I'm not really interested in critiquing or defending a certain author's (somewhat dated) opinion on certain issues. I'd rather discuss the issues on their own merits.

    That is, if you wish to dicuss the notion of 'genetic determinism', and/or the supposed role played by that supposed phenomenon in heredity and/or evolution, and/or the role that epigenetics plays in evolution, that would suit me far better.

    In that light, when you say--


    My answers to the authors critique of genetic determinism is, so what.

    I think that just about everybody has now denied and distanced themselves from the old, 'genetic determinism' model. The answer to your 'so what' is that the selectionist approach to evolution, being dependent upon Fisher, Haldane, and Wright's RM+NS model, does not hold water if those random mutations are not solely responsible for, and do not entirely compel, phenotypic traits and their variations. That is, how can random genetic mutations be the cause of evolution if genes are not the determining cause of traits? If, as modern science shows, 'genes' do not 'cause' traits, that is, do not compel and determine traits but only enable and facilitate their development, then how can random genetic mutation be said to be responsible for the origins of biological novelty? To enable and to facilitate is not the same as to cause.
    Mechanisms are compelling causes, not the conditions that enable them to operate. A forest fire is not caused by dry timber, although that does enable one; only a flame from a fire started by a match or a lightning bolt is the direct, immediate and compelling cause. If 'genes' are only the 'dry timber' wrt evolution and development, then what is the 'flame'?


    Evolution needs to act on hereditary information.

    How so? This sounds good, but what does it really mean? For one thing, evolution is an action, not an actor.


    Whether this hereditary information is genetic, protein, RNA, methylation patterns, or cell membranes, it does not change the fact that they all are hereditary.

    Again, meaning what? Pre-existing? That won't account for novelty, for origins, for evolution.


    A knowledge of epigenetic phenomenon only confirms that what is the hereditary unit is the ultimate source of selection.

    Says who? From wikipedia, 'epigenetics'--

    "Epigenetics is distinct from epigenesis, which is the long-accepted description of embryonic morphogenesis as a gradual process of increasing complexity, in which organs are formed de novo (as opposed to preformationism). However, because all of the cells in the body inherit the same DNA sequences (with a few exceptions, such as B cells), cellular differentiation processes crucial for epigenesis rely almost entirely on epigenetic rather than genetic inheritance from one cell generation to the next. [bold added]

    Since morphogenesis is responsible for the actual trait, and since the expressed trait is all that 'natural selection' has to work with, and since morphogenesis relies upon epigenetic, ('not genetic'), inheritance, then the 'gene' cannot be "the ultimate source of selection". Even assuming, [which I do not], that 'selection' means anything.


    This message is a reply to:
     Message 5 by mobioevo, posted 12-18-2007 10:50 PM mobioevo has not yet responded

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    AdminWounded
    Inactive Member


    Message 7 of 12 (441973)
    12-19-2007 1:12 PM
    Reply to: Message 6 by Elmer
    12-19-2007 8:23 AM


    Veering off topic
    I think your position on epigenetics and genetic determinism definitely deserve its own thread. Since you have said you don't wish to discuss the paper the OP is centred around you are clearly going to be going off topic in this thread.

    Could you maybe draft a PNT summarising your thoughts in this thread and the Macroevolution thread?

    TTFN,

    AW


    This message is a reply to:
     Message 6 by Elmer, posted 12-19-2007 8:23 AM Elmer has responded

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    RAZD
    Member (Idle past 304 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 8 of 12 (442002)
    12-19-2007 3:51 PM
    Reply to: Message 5 by mobioevo
    12-18-2007 10:50 PM


    I didn't add any quotes from the paper because I wanted others to read the paper and not just the quotes that I would write. You are probably right so I will do so in my next posts. Right now I wanted to define some of what the paper is concerned.

    The problem for me is that whenever anyone wants to claim that new studies have either invalidated or replaced evolution, that this doesn't affect all the cases where evolution has been validated. One of the others to make similar claims to this paper is Jeffery H Schwartz in "Missimg Links and "Sudden Origins" (see threads)

    My answers to the authors critique of genetic determinism is, so what. Evolution needs to act on hereditary information. Whether this hereditary information is genetic, protein, RNA, methylation patterns, or cell membranes, it does not change the fact that they all are hereditary.

    This is also why I use "hereditary traits" rather than "frequency of alleles" in discussing evolution. If it's hereditary and it contributes to selection then it is part of evolution.

    The author's argument for the paper being discussed is since there is more evidence that their are other forms of non-genetic inheritance will genetic determinism still survive. In the author's opinion no. He feels a more fully theory of the cell will develop out of epigenetic phenomenon.

    All this does in my mind is add to the theories involved in evolution, but doesn't take any away.

    Thus when we define the "theory of evolution" as the ∑(all theories) of how changes in hereditary traits occur in populations and are passed from generation to generation, we just have ∑n+1 = ∑n + 1 ... not very stunning when n = large.

    Thanks.

    Edited by RAZD, : last quote


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    This message is a reply to:
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    Elmer
    Member (Idle past 4803 days)
    Posts: 82
    Joined: 01-15-2007


    Message 9 of 12 (442017)
    12-19-2007 4:54 PM
    Reply to: Message 7 by AdminWounded
    12-19-2007 1:12 PM


    Re: Veering off topic
    Could the above post serve as the PNT required, under the heading, "Is 'genetic determinism' empirically valid, and is it essential to the "Modern Synthesis"? I've never started a thread in this forum, so I do not know how such things should be set up.

    This message is a reply to:
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    RAZD
    Member (Idle past 304 days)
    Posts: 20714
    From: the other end of the sidewalk
    Joined: 03-14-2004


    Message 10 of 12 (442021)
    12-19-2007 5:31 PM
    Reply to: Message 9 by Elmer
    12-19-2007 4:54 PM


    tips for newbies
    Go to Forum Proposed New Topics to post new topics.

    You fill it out just like a regular post, but it won't be accessible until it is promoted by an admin. Usually you need to say which forum, but this would be biological evolution.

    You can use peek or edit on your old post to copy it with coding and you can also use links to the original if you want.

    I'd ask mobioevo if he thinks it is off-topic as he seemed pretty open to me. Not that both threads couldn't go in different directions (evolve :D)

    Enjoy.


    Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

    we are limited in our ability to understand
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    RebelAAmericanOZen[Deist
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    This message is a reply to:
     Message 9 by Elmer, posted 12-19-2007 4:54 PM Elmer has not yet responded

      
    MartinV 
    Suspended Member (Idle past 4728 days)
    Posts: 502
    From: Slovakia, Bratislava
    Joined: 08-28-2006


    Message 11 of 12 (442466)
    12-21-2007 11:53 AM
    Reply to: Message 1 by mobioevo
    12-17-2007 7:14 PM


    Thank you for the link mobioevo. Generally speaking I agree with professor Strohman. His opinions are in accord with opinions of professor Zdenek Neubauer, Charles Uni Prague that modern biology is under the influence of "Fachidiots" (german term). Neubauer published his first researches in the Nature when he was only 24 years old microbiologist. But now he turned to be a strong opponent of neodarwinism.

    You know, you don't have to tell apart lion and tiger but you are still able to study their "evolution" comparing their DNA according neodarwinian paradigma.

    Strohman quotation of Feynmann is also ineresting:
    "Mind must be a sort of dynamical pattern, not so much founded in a neurological substrate as floating above it, independent above it".

    It is an interesting phenomenon that physicists are more open to transcedent ideas than biologists. But I wouldn't say that quantum mechanics is easier stuff than counting alleles in a population.

    Edited by MartinV, : No reason given.

    Edited by MartinV, : grammar


    This message is a reply to:
     Message 1 by mobioevo, posted 12-17-2007 7:14 PM mobioevo has not yet responded

      
    miosim
    Member (Idle past 4577 days)
    Posts: 57
    From: NH, USA
    Joined: 04-07-2007


    Message 12 of 12 (446314)
    01-05-2008 3:58 PM
    Reply to: Message 5 by mobioevo
    12-18-2007 10:50 PM


    mobioevo,

    In one of your posts you described the sexual reproduction in Paramecium , as an example of an epigenetic phenomenon.

    In my posts Why There Are Two Sexes Exist? I am using a similar example to illustrate a controversial hypothesis about two sexes emergence and mechanism of cell differentiation. I think the mechanism of cell differentiation is the most prominent example of epigenetic phenomenon.

    Would be interesting to have your opinion on the proposed hypothesis. The "technical" aspects of proposed mechanism you can find at DNA Asymmetric Gene Activity

    Edited by miosim, : No reason given.


    This message is a reply to:
     Message 5 by mobioevo, posted 12-18-2007 10:50 PM mobioevo has not yet responded

      
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