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  #101  
Old 30-03-2011, 03:39 PM
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snas (Stuart)
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Stuart,
Apart from everything else that you wrote, I disagree with you on the above...
Bacteria can't "developed" genes....
Bojan, I have to agree that I may have worded that better. You are quite correct, bacteria do not set out to "develop" genes.

Perhaps instead of

"Strep pneumoniae developed the genes to allow it to beef up its defences against our immune systems"

I could have written something more like:

"some Strep pneumoniae developed (by chance, not by intention or plan) the ability to produce a more robust external sugar capsule which gave them the ability to withstand human immune defences"

Still, while the bacteria did not set out to develop the genes, the genes must have developed for some reason. The more robust external capsule would not be present without the genetic information to code for it.

Craig, the "blind, unthinking, uncaring process" has no conscious intent. For example, I did not set out to develop immunity to a certain bacterium or virus, my body just did it as part of it's natural immune responses. (Not really a good example because developing an immune response like that is not an example of evolution, but you get the idea)

So at the "whole organism" level, there is no conscious intent. But at a much smaller level, down at the genes level things happen such as random mutations which may by pure chance happen to confer an increased chance of survival on the organism.

Stuart

Last edited by snas; 30-03-2011 at 03:51 PM.
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  #102  
Old 30-03-2011, 03:45 PM
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Originally Posted by avandonk View Post

The latest research has thrown up a new science called Epigenetics. This is where the environment an organism finds itself in switches off and switches on existing genes in your germ cells ie sperm and eggs.. It is all to do with the methylation of genes making them unreadable.
Yep, I am aware of this.. However this is much much "higher level".. way more complicated process than simple DNA mutation I was talking about earlier...
We have to start from somewhere
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  #103  
Old 30-03-2011, 05:58 PM
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Originally Posted by bojan View Post
Yep, I am aware of this.. However this is much much "higher level".. way more complicated process than simple DNA mutation I was talking about earlier...
We have to start from somewhere
Not at all
Quote:
Originally Posted by Wiki
In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters.
...
As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes. Consequently, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development.
..more ..
Quote:
Response to environment:
Not only do transcription factors act downstream of signaling cascades related to biological stimuli but they can also be downstream of signaling cascades involved in environmental stimuli. Examples include heat shock factor (HSF), which upregulates genes necessary for survival at higher temperatures, hypoxia inducible factor (HIF), which upregulates genes necessary for cell survival in low-oxygen environments, and sterol regulatory element binding protein (SREBP), which helps maintain proper lipid levels in the cell.
Not random .. induced by the environmental changes which can easily be non-random !

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  #104  
Old 30-03-2011, 06:52 PM
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Craig,
I think I disagree... I am afraid that this is all just the free use of metaphorical language to describe processes which are not known in detail (?)
But, I can't really comment any further, because this is beyond my understanding of the subject...
After all, I am just a humble RF electronics engineer, thinking about retirement ,
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  #105  
Old 31-03-2011, 10:35 AM
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Ok … found these words … they seem to encapsulate what we've collectively said however, I personally disagree that all genetic mutations are purely random, because there is clear recent evidence to the contrary. This aspect is important when considering the minimal subset of environmental conditions we think are necessary for the emergence of exo-life.

I also find that these words (and the concept), also assumes we know intimately beforehand, what is required for the survival of the organism and then conclude that if an organism survives over the long haul, it must therefore possess the survival characteristics we assumed in the first place.

In Darwin's day, this was obvious at the macro functional/feature level of a species. However, in modern times, we have discovered way more about the complexity of genetic interactions, their influences at the micro (DNA) level and what causes mutations. (Molecular Genetics).

For me, a large proportion of the diversity we see amongst life-forms, may be more a characteristic of not necessarily survival associated, but none-the-less, environmentally induced mutations. Perhaps its my own lack of knowledge, but I'm not sure Darwinian Evolution Theory addresses the reasons for propagation of what could easily be mutationally induced, non-essential characteristics (??)

As a result, I feel that there are other processes which run in parallel, (ie: not necessarily contrary to Darwinian Evolution), which have clearly operated since life emerged from the chaos.

What does this perspective tell us about the chances of life emerging elsewhere ? Frankly, I have no supportable ideas, other than I can see this thinking does support the concept that diversity, (which includes the superset encompassing the 'null' no-life outcome), may be way more susceptible to the initial environmental conditions from which life originally emerged once, than perhaps we can envisage. It also lends legitimacy to the possibility of extreme rarity of more than once instance of it.

There is a Hypothesis called 'Differential Susceptibility' which speculates that individuals vary in the degree they are affected by experiences, or qualities of the environment they are exposed to. These characteristics are then linked to susceptibility factors which can range from emotional states like temperamental anxiousness all the way 'down' to the protein/DNA level. (Mind you, it remains as a 'considered' hypothesis ).

Having made these statements, I find that the following words, do fairly describe the classical biological definitions pertaining to the role randomness plays in classical, traditional, Darwinian Evolution Theory:

Quote:
Randomness in biology:

The modern evolutionary synthesis ascribes the observed diversity of life to natural selection, in which some random genetic mutations are retained in the gene pool due to the non-random improved chance for survival and reproduction that those mutated genes confer on individuals who possess them.

The characteristics of an organism arise to some extent deterministically (e.g., under the influence of genes and the environment) and to some extent randomly. For example, the density of freckles that appear on a person's skin is controlled by genes and exposure to light; whereas the exact location of individual freckles seems to be random.
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  #106  
Old 02-04-2011, 08:03 AM
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Originally Posted by mjc View Post
I think I'm on board with what Bojan has been advocating - particularly with respect to the "no paradox" idea. I agree with Craig with respect to difficulties of language usage. There isn't any selfishness per se - nor any purpose or design - it just the way things tend to happen after the (physical) laws of nature pan out. When a mutation occurs its usually detrimental - sometimes its beneficial. In the case where its beneficial its because of what benefits this change has rather than what this change was "intended" to do that aids in the propagation of a species. But underlying all this is a bunch of genes - of which some are shared widely (between species) and the tendency is that there is a core bunch that do better than others. It doesn't matter what species survives or is demised - the only significant outcome is that some bunch of genes dominate - regardless of what host they contribute to the definition of.

Two observations I'd like to raise:-
1) Randomness - we can go down a dark road on that one, "God does not play dice" etc. But there are events that we cannot predict and the concept of randomness - with the appropriate mathematics works well (Gaussian and Poisson distributions, for example).
2) Life has a tendency to organise - which is counter to the over-all universe's tendency to transition from order to disorder. If I'm correct - you can always find a way of burning things that were alive.

Just some thoughts.

Mark C.
Hi Mark;

Have a look into Chaos Theory in particular, the emergence of self-organisation.
It really is truly fascinating !

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