Preadaptations

[Phronesis]

Regarding the potential random variation of dormant genes, like I said I'm no biologist, but is there not genetic variation on genes to contribute to fitness as well as dormant genes?

Yes there is genetic variation in genes that contribute to fitness, however, mutations that are detrimental to fitness are removed by selection. Neutral and beneficial mutations are selected. An example is the sequences divergence of sliding clamps of organisms in the various domains of life. Very little sequence similarity, yet they perform the same function.

Mutations in genes that do not contribute to fitness are not removed by selection, as they are all neutral with regards to fitness as they do not contribute to fitness. Thus, if a gene had a function and became dormant, selection does not buffer against mutations that will negatively affect its original function and the original function of the gene can be lost very easily due to the effect of randomness.

 

[Geriatrix]

Mutations in genes that do not contribute to fitness are not removed by selection, as they are all neutral with regards to fitness as they do not contribute to fitness. Thus, if a gene had a function and became dormant, selection does not buffer against mutations that will negatively affect its original function and the original function of the gene can be lost very easily due to the effect of randomness.

But the dorman genes, although slightly altered are not instantly outrite detroyed. Does that not leave room for future reactivation of dormant genes, even though they might be slightly altered?

 

[Phronesis]

Yes, that depends on how redundant the system is in how well it is able to buffer against the effect of random variation. Some mutations will completely destroy the function of a gene or perhaps hamper an entire signaling pathway. I would argue that in the long run, genes that do not contribute to fitness are far more likely to lose their original function as a result of random variation.

 

[cyghost]

And wouldn't that be a death blow to so called front loaded evolution which some theists argue for every now and then? I must remember this should I be in such a predicament again.

 

[Phronesis]

As explained to you over and over.... No. How is this relevant?

 

[Geriatrix]

I would argue that in the long run, genes that do not contribute to fitness are far more likely to lose their original function as a result of random variation.

How long?
Sorry, I couldn't resist.

 

[Phronesis]

How long?

That... I don't know . Probably gene dependent and the robustness of the system. Also most likely much quicker than genes that do contribute to fitness.

 

[cyghost]

As explained to you over and over.... No. How is this relevant?

I would argue that in the long run, genes that do not contribute to fitness are far more likely to lose their original function as a result of random variation.

And wouldn't that be a death blow to so called front loaded evolution which some theists argue for every now and then?

That's how and I am happy to see you are still wrong

 

[Phronesis]

The intriguing genome of the Trichoplax (Placozoa meaning flat animals):
Trichoplax Genome Sequenced: 'Rosetta Stone' For Understanding Evolution

Nice Pic


Place on the evolutionary tree​

Currently there is only one named species in the phylum: Trichoplax adhaerens.

It's a flattened blob, a few millimeters across and made up of a few thousand cells. It's main claim to fame is its remarkable simplicity: it is a multicellular animal that consists of only four apparent cell types, and the only obvious organization is into an upper and lower surface. The upper surface consists of a sheet of covering cells, while the lower surface contains two cell types: the gland cells that secrete digestive enzymes onto whatever the animal is sitting on, and the cylinder cells that absorb whatever nutrients are released. In between is a loose network of fiber cells that are responsible for the animal's movement.

Link
Nerves, sensory cells and muscle cells are absent.
Interestingly (from the link):

One other strange thing: in culture, Trichoplax is consistently asexual and reproduces by fission, but older cultures at high density begin to produce small motile presumptive sperm cells, and as individual animals desintegrate, they spew out ova. The two have never been observed to come together, though, so there is no fertilization, and while the ova may divide a half dozen times, they all eventually die. It is possible that there is another stage in the life cycle that is not viable under laboratory conditions and has never been observed.

The genome of this critter is even more fascinating.
From the nature article:
The Trichoplax genome and the nature of placozoans

Table 1 | Developmental transcription factors in the Trichoplax genome
Homeobox (Hox genes)

• A) ANTP-class: Trox-2 (Hox/ParaHox-like), Not, Dlx, Mnx, Hmx, Hex, Dbx and seven others.
• B) PRD-class (paired box and homeobox): PaxB, Pitx, Otp, Gsc and five others
• C) POU-class(POU domain and homeobox): POU class 4 (Brn-3), one other
• D) LIM-class (LIM domain and homeobox): islet, apterous, Lhx1/5 and one other
• E) SIX-class (sine oculis homeobox): Six3/6 and one other
• F) TALE-class: Pbx/Exd, Irx, Meis
• G) HNF-class: Hnf

Going down the list, what are the functions of these Hox genes?
1) Trox-2 (Hox/ParaHox-like)
Hox/paraHox-like genes are involved in axial patterning in bilaterarian organisms. Basically, they control the formation of the anterior–posterior (AP) axis. Function of Trox-2?

We speculate that Trox-2 functions within a hitherto unrecognized population of possibly multipotential peripheral stem cells that contribute to differentiated cells at the epithelial boundary of Trichoplax.

2) Not
In mice, Not controls the development of the caudal notochord. What is the notochord?
Wiki

The notochord is a flexible, rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In lower vertebrates, it persists throughout life as the main axial support of the body, while in higher vertebrates it is replaced by the vertebral column. The notochord is found on the ventral surface of the neural tube.

What does it do in this flat, simple organism?

The homeobox gene Not is highly conserved in Xenopus, chicken and zebrafish with an apparent role in notochord formation, which inspired the name of this distinct subfamily. Interestingly, Not genes are also well conserved in animals without notochord such as sea urchins, Drosophila or even Hydra, but appear to be highly derived in mammals. A search for homeobox genes in the placozoan Trichoplax adhaerens, one of the simplest organisms available today, revealed only two homeobox genes: a Not homologue and the previously described gene Trox-2, which is most similar to the Gsx subfamily of the Hox/ParaHox cluster genes. Not has a unique expression profile in Trichoplax. It is highly expressed in folds of intact animals and in the wounds of regenerating animals. The dynamic expression pattern of Trichoplax Not is discussed in comparison with the invariable expression pattern of Trox-2 and the putative secreted protein Secp1. The high sequence conservation of Not from Trichoplax to lower vertebrates, but not to mammals, represents a rare example of an apparent gene decay in the lineage leading to humans.

Interesting preadaptations .

Next, a look at the other Hox genes in this organism and their functions in higher animals.
Dlx, Mnx, Hmx,Hex, Dbx etc...

Hox genes video
Nice overview of Hox genes.

 

[alloytoo]

Exploring ignorance: genetic complexity and the hox genes

Article on Panda's Thumb

 

[Phronesis]

Saw that. Sure you will agree those too, are interesting preadaptations. Eg.

In other words, the original hypothesis was that a ‘dramatic change’ was required for limbs to develop. Such a position would be a much larger problem for evolutionary theory than finding that the re-use of a duplicated hox gene for limb evolution explains the origin and evolution of the tetrapod limb.

There is that word co-option again :

This form of co-option is a common evolutionary strategy, and in fact countless other instances of co-option show how prevalent this form of evolutionary variation is. While some may see this as disproving evolutionary theory because it is an ‘abrupt’ rather than a ‘gradual’ change, they are missing the point that evolution modified pre-existing variation to modify the secondary stage of fin formation to limb formation.

Co-option as a strategy for preadaptations .

 

[alloytoo]

Saw that. Sure you will agree those too, are interesting preadaptations. Eg.

There is that word co-option again :

Co-option as a strategy for preadaptations .

How does one distintuish preadaptation with neutral mutation?


In general neutral mutations (The majority) are not weeded out by natural selection because there is no negative consequence to their existance. Neither is there an immediate advantage.

However should conditions change, dormant mutations would then either become advantageous or negative.

I suppose you could say those neutral mutations that become positive are pre-adaptations.

Would those neutral mutations that become negative become pre-unadaptations?

 

[Phronesis]

Preadaptations are not necessarily neutral mutations. Neutral mutations are not necessarily preadaptations. Google and wiki can help you get an understanding.
The purpose of this thread:
If anyone come across any interesting findings, post it here .

 

[alloytoo]

Preadaptations are not necessarily neutral mutations. Neutral mutations are not necessarily preadaptations. Google and wiki can help you get an understanding.
The purpose of this thread:
If anyone come across any interesting findings, post it here .

Funny I thought I asked you.

(Std Disclaimer: in your own words, no quotemines or hyperlinks etc etc )

 

[Phronesis]

The purpose of this thread:
If anyone come across any interesting findings (wrt to preadaptations), post it here.

Std Disclaimer: If you do not know something, don't ask someone that you think does not know what he is talking about. Google and logic is your friend, and this is not the thread for people to give definitions of concepts of which there already exist. Do your own homework.

 

[cyghost]

Std Disclaimer: If you do not know something, don't ask someone that you think does not know what he is talking about. Google and logic is your friend, and this is not the thread for people to give definitions of concepts of which there already exist. Do your own homework.

At the risk of being branded an offtopic whore I still would like to make a comment on this. See it as positive criticism if at all possible.

This is a forum where we discuss things. Not a blog where loads and loads of links and copy and paste jobbies and things are attached only, interesting as it may be.

You would do well to actually answer some questions in your own words every now and then.

/just a thought.

 

[alloytoo]

At the risk of being branded an offtopic whore I still would like to make a comment on this. See it as positive criticism if at all possible.

This is a forum where we discuss things. Not a blog where loads and loads of links and copy and paste jobbies and things are attached only, interesting as it may be.

You would do well to actually answer some questions in your own words every now and then.

/just a thought.

Good thought.

 

[Phronesis]

MODS, a little here please.
This post contributes nothing (may be deleted)
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This post is off topic and needs to be moved to the appropriate thread (has been reported)
This post is off topic (may be deleted)
This post is off topic and needs to be moved to the correct thread (has been reported)

In this post the user feels he needs to criticize and mentions the following:

This is a forum where we discuss things. Not a blog where loads and loads of links and copy and paste jobbies and things are attached only, interesting as it may be.

By all means, discuss, discuss, discuss. This person did not contribute one on topic post, yet feels the need to criticize other people for not discussing anything. His comment above is divorced from reality and adds absolutely nothing to the topic at hand. Clearly the person is not interested in contributing anything useful, yet feels the need to criticize. This is highly inflammatory and only creates more heat than light.

The person also feels that he is justified in saying the following:

You would do well to actually answer some questions in your own words every now and then.

This is also divorced from reality, a quick survey of the thread will demonstrate it clearly. Again, this person does not contribute, feels the need to criticize, and generates friction. Highly malicious.

In this post the user agrees with obviously false statements and this amounts to nothing more than sycophantic behavior.
This is of course not the first time that it happened. For example:
1
2
3
These (to mention a few) all attest to this kind of behavior.

This type of behavior is not condoned in other forums, why should it be allowed here?

The replies to this post in this thread will provide ample evidence how a thread can spiral out of control. All that was needed was the removal of a few off topic comments that created more heat than light.

 

[cyghost]

you seem to be looking for a position as mod now?

I wish you well although this new removal and deletion of posts seems a tad draconian in my oh so humble opinion. Do note it is the nature of threads to drift off topic. I hope your new measures to keep it on topic and only on topic works for you.

Do you really want to be subscribing to what others may or may not post in this way though? If you get what you are asking for here you will be a lonely little poster.

So why don't you instead go clean up all the other threads as well and make your little demands of having posts removed? there is quite a few for you and it will keep you busy for a while. Concentrate on threads where you posted first.

You forgot that now you will have to make another post to have post 38 removed as well?


to any mod: you may safely remove any and all of my posts (including this one) as you see fit and won't get a peep out of me. Please do so at your own behest though and where it is actually called for, not on some petulant, childish cry for attention.

malicious indeed

 

[alloytoo]

Mods A little attention here:

This post appears to be petty, vindictive and above all off topic.

It still doesn't answer my question of how preadaptation is (at a gross level) distinuishable from neutral mutations becoming benificial due to a change in enviroment as described by the hypothesis of puntuated equilibrium.

I'm not quite sure what all the fuss is about then, it's really nothing more than glorified natural selection finding niches to exploit and occassionally causing speciation.