Genetic Toolkits and Multicellularity

[rwenzori]

A good idea methinks. Grease monkey ftw. Have you ever noticed Grease monkeys look like windmills? like little machines?

LOL! Intentional little agents, aren't they?

 

[Phronesis]

And so the mindless invasion continues.

 

[w1z4rd]

LOL! Intentional little agents, aren't they?

Yeah, they pre-adapt to every situation.

 

[alloytoo]

Seems pretty obvious to the non-casual observer that Prhony doesn't actually want to engage in discussion, but would prefer to insult folks who make observations.

None the less, since willy nilly posting links is standard phrony procedure I'll post one of my own:

Organismal size over evolutionary time is a constrained stochastic property.

Note the interesting "Blogging on Peer reviewed research" logo.

 

[Phronesis]

Organismal size over evolutionary time is a constrained stochastic property.

Note the interesting "Blogging on Peer reviewed research" logo.

See, the diiference is I read what PZ said. You most definately did not even to attempt to read this entry, which in a way is related.

BTW, anyone can use that "Blogging on Peer reviewed research" logo. Nothing really special about it.

Here are the points again:
1) Most of the tools for the hedghog signaling pathway toolkit are present in prokaryotes (bacteria and archaea). Note that this toolkit plays a crucial role in cell patterning, cell proliferation and participates in the development of tissues and organs during the stages of animal development.
2) Note that the origin of multicellular body plans roughly coincide with an increase in atmospheric oxygen pressure (this is what is discussed in the paper you never discussed, just alluded to) as well as the first bona fide hedgling (Read up on hedgelings). Remember, hedglings are the only examples of post-translational sterolation (addition of cholesterol) of proteins in contempory biology. Why is this interesting? Well, oxygen is needed for cholesterol synthesis, more importantly, oxygen is needed for placing the hydroxyl group in the 3-position of cholesterol which plays a crucial role in subsequent transformations (including sterolation). Thus, while large parts of the hh-signaling pathway was present, a little extra oxygen was needed to unlock multicellular signaling capabilities of hedglings.
3) Therefore, words like “pre-existing”, “latent” and “potential” seem apt in describing the hedghog signaling pathway and the unfolding of multicellular body plans in relation to the increase in atmospheric oxygen pressure. “Innovation” perhaps not so much, seeing that only real innovation was bought on about by life itself namely the increase in atmospheric oxygen. This increase in atmospheric oxygen in turn seemed to have unlocked the pathways to multicellular body plans (>3 cell types).

Point three is perhaps relevant to why the author chose those words.

4) In addition to point 3, not only were a bulk of the toolkits for multicellularity present in prokaryotes, but the increase in oxygen bought about by life unlocked the signaling capabilities of the hedgehog signaling pathway which relies on oxygen. Now to further understand why this is, consider the following article:
Acquisti C, J Kleffe & S Collins (2007). Oxygen content of transmembrane proteins over macroevolutionary time scales. Nature 445: 47-52.

Conclusion
In this study, we have shown that transmembrane proteins can be divided into two groups according to their oxygen content. Independent topology prediction reveals these same two groups. We have shown that the proportion of receptors to channels increases over time and coincides with a change in cellular organization. In addition, older proteomes contain less oxygen per residue and produce fewer high-oxygen proteins. Taken together, this suggests that oxygen use was selected against in these proteomes. This constraint lessened over time as the concentration of atmospheric oxygen increased, which resulted in the extracellular domains of transmembrane proteins increasing in size over time faster than the internal domains. Consequently, we propose the following hypothetical mechanism: atmospheric oxygen concentration constrained the topology of ancient transmembrane proteins by limiting the number and size of external domains that could be formed. Any mechanistic explanation of how atmospheric oxygen concentration limited the number and size of external domains is necessarily speculative. One possibility is that it was simply futile to exude large, oxygen-rich domains in a reducing atmosphere where oxidized amino acids could have been rapidly reduced. In this case, the use of oxygen-rich amino acids would have been selected against by natural selection because protein structure would have been more robust when fewer oxidized residues were exuded.

Stated differently, eukaryotic proteomes were more receptive and robust in accepting oxygen-rich amino acids.

Linking this to the timing of appearance of eukaryotic cells implies that the oxygen content is preferentially increased in receptors, and that this increase affects receptor function. This makes intuitive sense because the external domains of receptors required for communication have specific secondary and tertiary structures, many of which have some minimum size [23]. This is consistent with the bias we found towards having both longer and more oxygen-dense external domains in receptors relative to channels, and with the fact that eukaryotic genomes encode more and larger receptors than do prokaryotes. This suggests that protein oxygen content itself is important, rather than being a proxy for some other property.

Therefore, eukaryote proteomes were more receptive of oxygen-rich amino acids, this in turn aided in the development of secondary and tertiary structures needed for communication. A pre-existing property of eukaryotes was able to take more advantage of the change in atmospheric oxygen pressure. This lead to the unfolding of toolkits for multicellular body plans. But this change was bought on by life itself (increase in atmospheric oxygen pressure).

So yes, the author of the article can consider words like "pre-existing" and "latent evolutionary potential" to be apt in describing these transitions.

See, the questions for discussion of this thread are the following (but not limited to it):
1) Why does an increase in atmospheric oxygen seem to have the effect of driving eukaryotic multilcellular life but not bacteria and archaea? Is an intrinsic and latent property present in this domain?
2) Gene loss vs innovation: How much gene loss and how much innovation (not just co-option) has occured from the LUCA? (Speculating)
3) Why did all the toolkit parts for the hh-pathway converge on a single sterolation pathway when so many other possibilities are available? Or is it the optimal possibility and random variation and selection processes used by life hit a global optimum?

I am willing to discuss any of the above if you don't act like a total mindless troll. The mods are not doing anything to curb that behaviour, why should I be nice to them if they (yet again) behave like little mindless trolls?

 

[w1z4rd]

Seems pretty obvious to the non-casual observer that Prhony doesn't actually want to engage in discussion, but would prefer to insult folks who make observations.

None the less, since willy nilly posting links is standard phrony procedure I'll post one of my own:

Organismal size over evolutionary time is a constrained stochastic property.

Note the interesting "Blogging on Peer reviewed research" logo.

That is an interesting "peer review" logo. I wonder how that is managed?

 

[alloytoo]

See, the diiference is I read what PZ said. You most definately did not even to attempt to read this entry, which in a way is related.

Of course not, I read PZ's entry which explained things nicely (which is why he is both a practicing researcher and educator).

BTW, anyone can use that "Blogging on Peer reviewed research" logo. Nothing really special about it.

Actually there's a code of conduct related to the logo. that shouldn't pose a problem for you though.

 

[w1z4rd]

Actually there's a code of conduct related to the logo. that shouldn't pose a problem for you though.

 

[Phronesis]

Of course not, I read PZ's entry which explained things nicely (which is why he is both a practicing researcher and educator).

You admit to not even reading this entry. The questions have been posed and laid out around the entry. You choose to ignore them, and that constitutes nothing more than trolling. Are you actually going to read the post? If not, please troll on other threads and keep out of this thank you . I'll post th relevance of the entry again for you to concentrate on.

Here are the points again:
1) Most of the tools for the hedghog signaling pathway toolkit are present in prokaryotes (bacteria and archaea). Note that this toolkit plays a crucial role in cell patterning, cell proliferation and participates in the development of tissues and organs during the stages of animal development.
2) Note that the origin of multicellular body plans roughly coincide with an increase in atmospheric oxygen pressure (this is what is discussed in the paper you never discussed, just alluded to) as well as the first bona fide hedgling (Read up on hedgelings). Remember, hedglings are the only examples of post-translational sterolation (addition of cholesterol) of proteins in contempory biology. Why is this interesting? Well, oxygen is needed for cholesterol synthesis, more importantly, oxygen is needed for placing the hydroxyl group in the 3-position of cholesterol which plays a crucial role in subsequent transformations (including sterolation). Thus, while large parts of the hh-signaling pathway was present, a little extra oxygen was needed to unlock multicellular signaling capabilities of hedglings.
3) Therefore, words like “pre-existing”, “latent” and “potential” seem apt in describing the hedghog signaling pathway and the unfolding of multicellular body plans in relation to the increase in atmospheric oxygen pressure. “Innovation” perhaps not so much, seeing that only real innovation was bought on about by life itself namely the increase in atmospheric oxygen. This increase in atmospheric oxygen in turn seemed to have unlocked the pathways to multicellular body plans (>3 cell types).

Point three is perhaps relevant to why the author chose those words.

4) In addition to point 3, not only were a bulk of the toolkits for multicellularity present in prokaryotes, but the increase in oxygen bought about by life unlocked the signaling capabilities of the hedgehog signaling pathway which relies on oxygen. Now to further understand why this is, consider the following article:
Acquisti C, J Kleffe & S Collins (2007). Oxygen content of transmembrane proteins over macroevolutionary time scales. Nature 445: 47-52.

Conclusion
In this study, we have shown that transmembrane proteins can be divided into two groups according to their oxygen content. Independent topology prediction reveals these same two groups. We have shown that the proportion of receptors to channels increases over time and coincides with a change in cellular organization. In addition, older proteomes contain less oxygen per residue and produce fewer high-oxygen proteins. Taken together, this suggests that oxygen use was selected against in these proteomes. This constraint lessened over time as the concentration of atmospheric oxygen increased, which resulted in the extracellular domains of transmembrane proteins increasing in size over time faster than the internal domains. Consequently, we propose the following hypothetical mechanism: atmospheric oxygen concentration constrained the topology of ancient transmembrane proteins by limiting the number and size of external domains that could be formed. Any mechanistic explanation of how atmospheric oxygen concentration limited the number and size of external domains is necessarily speculative. One possibility is that it was simply futile to exude large, oxygen-rich domains in a reducing atmosphere where oxidized amino acids could have been rapidly reduced. In this case, the use of oxygen-rich amino acids would have been selected against by natural selection because protein structure would have been more robust when fewer oxidized residues were exuded.

Stated differently, eukaryotic proteomes were more receptive and robust in accepting oxygen-rich amino acids.

Linking this to the timing of appearance of eukaryotic cells implies that the oxygen content is preferentially increased in receptors, and that this increase affects receptor function. This makes intuitive sense because the external domains of receptors required for communication have specific secondary and tertiary structures, many of which have some minimum size [23]. This is consistent with the bias we found towards having both longer and more oxygen-dense external domains in receptors relative to channels, and with the fact that eukaryotic genomes encode more and larger receptors than do prokaryotes. This suggests that protein oxygen content itself is important, rather than being a proxy for some other property.

Therefore, eukaryote proteomes were more receptive of oxygen-rich amino acids, this in turn aided in the development of secondary and tertiary structures needed for communication. A pre-existing property of eukaryotes was able to take more advantage of the change in atmospheric oxygen pressure. This lead to the unfolding of toolkits for multicellular body plans. But this change was bought on by life itself (increase in atmospheric oxygen pressure).

So yes, the author of the article can consider words like "pre-existing" and "latent evolutionary potential" to be apt in describing these transitions.

See, the questions for discussion of this thread are the following (but not limited to it):
1) Why does an increase in atmospheric oxygen seem to have the effect of driving eukaryotic multilcellular life but not bacteria and archaea? Is an intrinsic and latent property present in this domain?
2) Gene loss vs innovation: How much gene loss and how much innovation (not just co-option) has occured from the LUCA? (Speculating)
3) Why did all the toolkit parts for the hh-pathway converge on a single sterolation pathway when so many other possibilities are available? Or is it the optimal possibility and random variation and selection processes used by life hit a global optimum?

I am willing to discuss any of the above if you don't act like a total mindless troll. The mods are not doing anything to curb that behaviour, why should I be nice to them if they (yet again) behave like little mindless trolls?

 

[alloytoo]

I'll post th relevance of the entry again for you to concentrate on.

Bit like trolling that, persistant reposting, almost like spam.....

I am willing to discuss any of the above if you don't act like a total mindless troll. The mods are not doing anything to curb that behaviour, why should I be nice to them if they (yet again) behave like little mindless trolls?

Simplified summary? Not more than 10 lines? (Generous today, normally would say 5)

 

[Phronesis]

Bit like trolling that, persistant reposting, almost like spam.....



Simplified summary? Not more than 10 lines? (Generous today, normally would say 5)

Sorry, I don't cater for mindless trolls looking for superficial summaries. Deal with the depth of the questions or stop trolling.

 

[alloytoo]

Sorry, I don't cater for mindless trolls looking for superficial summaries. Deal with the depth of the questions or stop trolling.

Oh dear, sorry, forgot, summaries are beneath you, tsk, tsk.

Here's the rub, only a few of us (oh the patient, the saintly few) actually bother to reply to you at all, and we ask, repeated (with celestial patience) that you dumb it down for the IT/broadband forum crowd..

This isn't a science blog, summarize it for the rest of us, or post elsewhere. What you're doing is blogging in the forums (or trolling to some)

 

[Phronesis]

Oh dear, sorry, forgot, summaries are beneath you, tsk, tsk.

Here's the rub, only a few of us (oh the patient, the saintly few) actually bother to reply to you at all, and we ask, repeated (with celestial patience) that you dumb it down for the IT/broadband forum crowd..

This isn't a science blog, summarize it for the rest of us, or post elsewhere. What you're doing is blogging in the forums (or trolling to some)

What a candid admission that you are in fact clueless with regards to biology, yet feel the need to comment on my understanding as well as what science is. Please don't insult others by implying that they do not understand what is being said. Don't project your ignorance onto others . And, yes, this is not the only place I post to try and get a discussion going. This is however the only place were your (and others') trolling behaviour seem to be the norm. Don't you think it is about time you just post in threads that you actually do have a vague idea about what's going on instead of just stalking me and trolling my threads?

 

[alloytoo]

What a candid admission that you are in fact clueless with regards to biology, yet feel the need to comment on my understanding as well as what science is. Please don't insult others by implying that they do not understand what is being said. Don't project your ignorance onto others . And, yes, this is not the only place I post to try and get a discussion going. This is however the only place were your (and others') trolling behaviour seem to be the norm. Don't you think it is about time you just post in threads that you actually do have a vague idea about what's going on instead of just stalking me and trolling my threads?

Oh deary me, more personal derision, for shame.

Clearly you are being less than successful in getting a discussion going, especially so as you refuse to engage people in a meaningful manner.

 

[Phronesis]

Oh deary me, more personal derision, for shame.

Clearly you are being less than successful in getting a discussion going, especially so as you refuse to engage people in a meaningful manner.

Lol, sorry matey, discussed these things in other forums with out any animosity or mud-slinging. You do the math.

 

[w1z4rd]

Lol, sorry matey, discussed these things in other forums with out any animosity or mud-slinging. You do the math.

Care to share the links?

 

[alloytoo]

Lol, sorry matey, discussed these things in other forums with out any animosity or mud-slinging. You do the math.

Are they IT/networking sites, or dedicated biology/creationists sites?

 

[Phronesis]

If you two actually read the posts in the threads you comment in you will find them. Don't show your ignorance so openly.
here, here or here.

 

[alloytoo]

If you two actually read the posts in the threads you comment in you will find them. Don't show your ignorance so openly.
here, here or here.

Ah, none of them appear to IT/Broadband related.

Why then is phrony trolling here one wonders?

W1zard old chap.

The "Preadaptations" thread in at Dawkins seemed to be abandoned in November, the one in science forums in September and the majority poster on the prhonies current threads at sciforums is prhony.

It would seem that we're more willing to engage prhony than others, but that he doesn't really want to engage with us.

 

[Phronesis]

Ah, none of them appear to IT/Broadband related.

Why then is phrony trolling here one wonders?

Nice South African site about South African news and South African Broadband. I don't pretend to know much about IT, therefor I do not post in IT sections telling people what IT is and what it is not. Trolling? Talk about genetic toolkits in the science section of an IT site is trolling now? Logic?

Here is the problem for you. These topics have been discussed in other forums without any animosity or mud-slinging. Why is it that here the main protaganists for such behaviour are you, wizzy, cyghost and rwenzori? You do the math . Pretend to know what science is but like to fling mud...mmmm pretenders. I guess that is the kind of behaviour one can expect from those who really truely believe it in their hearts that all our actions in the greater scheme of things is pointless. Sad really.