Biomolecular machines

Science... unfortunately for you, has a lot of teleological implications.
 
Only if you hold on to an incoherent and antiscientific outlook on life...Why your cute incoherent "Sh|t happens" "philosophy" does indeed look like it is antiscientific and self-defeating.
That also explains (in part anyway) the continued aversion you (and others probably) have for biomolecular machines... you know those things that make you who you are and science is discoveing how they do work...

Shame, have "Sh|t happens" "philosophy", don't want science. But, before you drag this thread down to a PD-type squabble (goodness knows you are trying hard). More marvelous machines :p:

[ame]http://www.youtube.com/watch?v=-zsEepV0N-I[/ame]

[ame]http://www.youtube.com/watch?v=LQD65eMHHvI[/ame]

[ame]http://www.youtube.com/watch?v=J8lhPt6V-yM[/ame]
 
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Communication on a molecular level ...sexy...

Sex Talk Revelations Of The Lonely Y Chromosome: Communication Between Male And Female Occurs In Our Innermost Beings

ScienceDaily (Sep. 14, 2009) — New findings from the University of Leicester Department of Genetics reveal for the first time that the male and female do truly communicate –at least at the fundamental genetic level.
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The research counters scientific theory that the X and Y chromosomes -- that define the sexes -- did not communicate at all.

The research is funded by the Wellcome Trust, and published in The American Journal of Human Genetics. In it Dr Zoë Rosser and colleagues have shown that exchange of DNA does actually occur between the X and Y in the regions previously thought to be completely isolated.

Professor Mark Jobling, who led the study, said: “Recently it was shown that the Y chromosome can talk to itself – swapping bits of DNA from one region to another, and potentially giving it a way to fix mutations that might affect male fertility. In this new research we’ve now shown that it actually maintains a genetic conversation with the X chromosome, potentially giving it a way to fix other kinds of mutations, too. So, maybe it’s not quite the dysfunctional loner we have always imagined it to be.”

The X and Y chromosomes have a vital role- sex is determined by them. Apart from the 22 pairs of regular chromosomes all of us share, women have two X chromosomes, while men have only one X but also the smaller Y chromosome. It’s the Y that determines maleness by triggering development of testes rather than ovaries in the early embryo.

Professor Jobling said: “These days the X and Y are a very odd couple, but long ago, before mammals evolved, they were an ordinary pair of identical chromosomes, exchanging DNA in a companionable way through the process of genetic recombination. However, once the Y chromosome took on the job of determining maleness, they stopped talking to each other. The X remained much the same, but the Y set out on a path of degeneration that saw it lose many of its genes and shrink to about one third the size of the X. Some scientists have predicted that it will eventually vanish altogether."

“These new findings from the Department of Genetics of the University of Leicester now challenge this interpretation of the Y chromosome’s fate,” he added.

The Leicester researchers discovered that the conversation between the X and Y chromosome goes both ways, and it’s also clear that mutations arising on a decaying Y chromosome can be passed to the X – the Y chromosome’s revenge, perhaps. Future work will assess how widespread X-Y exchanges have been during evolution, and what the likely functional effects might be.
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Karl Marx on Darwin:

"Not only is a death blow dealt here for the first time to 'Teleology' in the natural sciences but their rational meaning is empirically explained"
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Pssst, rwenzori... thread about biomolecular machines. Btw, Looks like Darwin was a bit of a teleologist himself

Was evolution at risk of not being scientifically stable?
Evolution still scientifically stable
Monash University's Professor Trevor Lithgow said the breakthrough, funded by the Australian Research Council and published recently in the prestigious journal PNAS, provides a blueprint for a general understanding of the evolution of the "machinery" of our cells.

"Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial." Professor Lithgow said.

A non-Darwinian explanation, from believers of Intelligent Design, proposed these complex machines to be "irreducibly complex". In other words they are so neatly complex and complete that they couldn't have evolved but rather must have been designed by an intelligent entity.

"Our research shows that these machines although complete and complex, were a result of evolution.
Simple ''core'' machines were established in the first eukaryotes by drawing on pre-existing proteins that had previously provided distinct, simplistic functions. They therefore stand as proof that Darwin's theory of evolution breaks down at the molecular level," Professor Lithgow said.

As a model system, the research focussed on one specific molecular machine, the TIM complex, which transports proteins into mitochondria. Mitochondria are a compartment of human cells that serve as the energy-producing 'powerhouses'. At a very early stage in evolution, mitochondria were derived from bacteria that lived within the first eukaryotic cells.

"Our cells literally are chimeras of a "host" cell and these intracellular bacteria. Yet bacteria don't have TIM complexes - to understand where the TIM complex came from we simply applied scientific reasoning and looked at a modern-day bacterium akin to the organism that gave rise to mitochondria." Professor Lithgow said.

The group looked at the bacterium Caulobacter crescentus and found bacterial proteins related to the components of the mitochondrial TIM complex. They then showed that these bacterial proteins are not found as part of protein transport machines.

"François Jacob described evolution as a tinkerer, cobbling together proteins of one function to yield more complex machines capable of new functions." Professor Lithgow said.

"Our work describes a perfect example of Jacob's proposition, and shows that Darwin's theory of evolution beautifully explains how molecular machines came to be."
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Even with statements like these, the usual pointless ponderers' continued aversion for biomolecular machines and complete abscence of posts ABOUT them continues to be fascinating. Maybe it is the biased nature of evolution? Maybe they are just not interested in science as evidenced by rwenzori's lack of interest and labeling science as "sh|t that happens"? What is wrong guys, I thought you were all pro-science (whatever you think that means)?
 
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Executioner caspases and programmed cell death signaling

How Proteins Talk To Each Other

ScienceDaily (Sep. 21, 2009) — Investigators at Burnham Institute for Medical Research (Burnham) have identified novel cleavage sites for the enzyme caspase-3 (an enzyme that proteolytically cleaves target proteins). Using an advanced proteomic technique called N-terminomics, Guy Salvesen, Ph.D., professor and director of the Apoptosis and Cell Death Research program of Burnham’s NCI-designated Cancer Center, and colleagues determined the cleavage sites on target proteins and found, contrary to previous understanding, that caspase-3 targets α-helices as well as unstructured loops.
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In addition, researchers found that caspase-3 and the substrates it binds to co-evolved. The paper was published on September 20 in the journal Nature Structural & Molecular Biology.

Prior to this study, scientists believed that proteases primarily cleave in unstructured loops, unstable parts of proteins that are readily accessible. The discovery that caspase-3 also cleaves α-helices contradicts a current dogma and offers new insights into protein signaling pathways.

“This was a big surprise because there shouldn’t be anything for a protease to grab onto in a helix,” said Dr. Salvesen. “We found that the basic concept that they don’t cleave to helices is wrong. However, though we’ve found that proteases can cleave helices, we don’t believe that’s their biological function.”

In addition to determining cleavage sites, the team also determined which interactions were “biologically significant.” In other words which cleavages altered the function of the target protein and which ones had little impact.

The team tested the human caspase-3 and the Staphylococcal protease glutamyl endopeptidase (GluC) against the Escherichia coli (E. coli) proteosome. In a second set, the human caspase substrate was challenged with human caspase-3 . The researchers found cleavage sites using N-terminal proteomics (N-terminomics), in which cleaved substrates are tagged at an exposed edge (N-terminal) and analyzed though mass spectrometry. The data from these assays were then matched against lists of substrates in the Protein Data Bank. Notably, caspase-3 did not cleave E. coli proteins as effectively as it did human proteins. However, when hybrid human/E. coli proteins were constructed, cleavage was greatly improved, leading researchers to conclude that caspase-3 co-evolved with its human substrates.

Because they alter the functions of other proteins, proteases like caspase-3 are critical to cell signaling. Understanding how and where they interface with target proteins enhances our ability to understand the progress of diseases.
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It is impossible to believe that such intricate precise "machines" out of their own initiative evolved considering that there are so many millions of other similar machines for different processes that function so specifically and precisely also. It is like winning every lottery all the time.
I imagine it must be like outting all the components of a rolex into a box and jiggling it for whatever time it much justify the possibility of the watchnot only coming together, ticking precisely on time, having a symbiotic function to unrelated life and also having a life of its own.
That is the most tremendous amount of luck, it is too much to ask to believe that such things thought themselves up out of necessity to survive, especially that it takes so many millions of years to evolve to that stage, they would have long been extinct anyway. It is like believing a frog turns into a prince if you add the magic ingredient: Time, lots and lots of time or thyme cos it doesn't seem to make a difference
 
Jenemesis said:
It is impossible to believe that such intricate precise "machines" out of their own initiative evolved considering that there are so many millions of other similar machines for different processes that function so specifically and precisely also. It is like winning every lottery all the time.
I imagine it must be like outting all the components of a rolex into a box and jiggling it for whatever time it much justify the possibility of the watchnot only coming together, ticking precisely on time, having a symbiotic function to unrelated life and also having a life of its own.
That is the most tremendous amount of luck, it is too much to ask to believe that such things thought themselves up out of necessity to survive, especially that it takes so many millions of years to evolve to that stage, they would have long been extinct anyway. It is like believing a frog turns into a prince if you add the magic ingredient: Time, lots and lots of time or thyme cos it doesn't seem to make a difference
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Yeah, it is kind of hard to believe that only random variation and natural selection can result in such precision. Especially when natural selection does nothing. Unless of course natural selection and the fitness landscapes are a bit rigged and biased in the first place towards the emergence of these precise structures :p.
 
Phronesis said:
Unless of course natural selection and the fitness landscapes are a bit rigged and biased in the first place towards the emergence of these precise structures :p.
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Rigged by whom or what? Aliens? Pretzlpakit? Bebeh Jebus? Is this religion in the science section again?
 
rwenzori said:
Rigged by whom or what? Aliens? Pretzlpakit? Bebeh Jebus? Is this religion in the science section again?
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Yes, and keep your anti-scientific "sh|t happens" "everything just is" nonsense and your religion-related tidbits out of here as well ;).
 
Phronesis said:
Yes, and keep your anti-scientific "sh|t happens" "everything just is" nonsense and your religion-related tidbits out of here as well ;).
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Oh no. They lie at the heart of science. To deny them is to assume a creator and divine purpose, for which there is, of course, not the slightest evidence.

:p
 
rwenzori said:
Oh no. They lie at the heart of science. To deny them is to assume a creator and divine purpose, for which there is, of course, not the slightest evidence.

:p
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To deny them is to assume a creator and divine purpose? Haha, try harder at keeping your anti-scientific "sh|t happens" "everything just is" nonsense from this section. As is, you have not contributed much anyway. What are you doing here again besides trolling?

Also, there is also no scientific evidence that you have mind of course. Should we assume you don't have a mind in order to be scientific and assume that the "everything just is", "sh|t happens" structure we call the brain just happens to pop out words for which there is no scientific evidence of being intelligent? You are of course welcome to present scientific evidence that you have a mind and is capabale of thinking and being intelligent. Waiting....
 
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Phronesis said:
To deny them is to assume a creator and divine purpose? Haha, try harder at keeping your anti-scientific "sh|t happens" "everything just is" nonsense from this section. As is, you have not contributed much anyway. What are you doing here again besides trolling?

Also, there is also no scientific evidence that you have mind of course. Should we assume you don't have a mind in order to be scientific and assume that the "everything just is", "sh|t happens" structure we call the brain just happens to pop out words for which there is no scientific evidence of being intelligent? you are of course welcome to present scientific evidence that you have a mind and is capabale of thinking and being intelligent. Waiting....
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Don't read it all wrong, old fruit. It is a position of non-assumption, a position stating that there is nothing unless demonstrated or proven. Unlike your consistent, credulous, "Wow! Check out what Bebeh Jebus did...". Don't expect more, as in your "set out a positive argument for atheism" whine. You cannot demonstrate any need to posit any purpose to anything in the universe, nor any need to posit anything other than the material and chance in the development of humanity. To repeat, "everything just is" and "sh|t happens".

PS wotch dat speling dere!
 
rwenzori said:
Don't read it all wrong, old fruit. It is a position of non-assumption, a position stating that there is nothing unless demonstrated or proven.
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I can see why you would like to hold such a position in general and with regards to your own mind. Like you said: "there is nothing unless demonstrated or proven". Welcome to bring some scientific evidence that you do have a mind ;).


rwenzori said:
Don't expect more, as in your "set out a positive argument for atheism" whine.
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I am not expecting any positive, coherent and non self-refuting arguments for atheism because there aren't any.


rwenzori said:
You cannot demonstrate any need to posit any purpose to anything in the universe, nor any need to posit anything other than the material and chance in the development of humanity. To repeat, "everything just is" and "sh|t happens".
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That is just plain old metaphysical materialist rambling. There is nothing scientific about it. It is just a philosophical outlook. And as a philosophical outlook,"everything just is" and "sh|t happens" is just plain anti-scientific, self-refuting and incoherent nonsense. You are welcome to sell that kind of nonsense in the PD section, but keep it out of the science section as it adds nothing and is laughably anti-scientific. Now if you want to keep on rambling about your materialistic metaphysics nonsense in the science section, I suggest you and your ilk don't moan when Aristotelian-Thomistic ideas are introduced.

Now can we expect you to actually contribute to this section? Waiting...
 
Phronesis said:
Now can we expect you to actually contribute to this section? Waiting...
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I regard crap-busting your incessant attempts to punt your ID nonsense as a significant contribution. Now can we expect you to actually contribute something other than said pseudo-scientific ID evangelising to this section? Waiting...
 
Soo.... worthless generalizations and spouting anti-scientific materialistic "everything just is" and "sh|t happens" nonsense is what you do? In the science section? Wow, who woulda thought.

And I thought you guys were being all intellectual and pro-science...
 
Phronesis said:
Soo.... worthless generalizations and spouting anti-scientific materialistic "everything just is" and "sh|t happens" nonsense is what you do? In the science section? Wow, who woulda thought.

And I thought you guys were being all intellectual and pro-science...
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Oh, I forgot. Exposing your plagiarism and lies too. After all, intellectual dishonesty and touting the work of others as your own are hardly very scientific, are they?
:eek:
 
rwenzori said:
Oh, I forgot. Exposing your plagiarism and lies too. After all, intellectual dishonesty and touting the work of others as your own are hardly very scientific, are they?
:eek:
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Ah, more worthless generalizations. Got anything new? Like actually contributing to a thread?
 
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