Rethinking junk DNA

[Phronesis]

Grow up .

 

[Palimino]

If something reproduces and is successful, it forms part of the next population, reprodcing again.

Feedback. That’s what I said.

Who said that? How about a global maximum being reached?

I did. Do you disagree?

Global maximum. Like you sharks and crocodile example?

If there is no threat to survival (like sharks and crocodiles), there is no reason to evolve. Otherwise you continue evolving (there is no global maximum). Individual’s which survive, pass-on their genes (and evolve). Darwin 101.

 

[Phronesis]

Feedback. That’s what I said.

So what is your problem? There is feedback in the diagram btw. Mutations and recombination do occur randomly.

I did. Do you disagree?

Differentiate between " until suitability to purpose occurs" and "reached a global maximum on the evolutionary landscape". Perhaps we are saying the same thing?

If there is no threat to survival (like sharks and crocodiles), there is no reason to evolve.

Hence...global maximum for a particular niche.

Otherwise you continue evolving (there is no global maximum). Individual’s which survive, pass-on their genes (and evolve). Darwin 101.

They still do when they reach a global maximum, they might just hover around the gloal maximum with minor variation here and there...like sharks and crocodiles.

Darwin 101? Which University gives that course? How about zoology there... or biology....or biochemistry....or genetics....

 

[Palimino]

So what is your problem? There is feedback in the diagram btw. Mutations and recombination do occur randomly.

A feedback loop would go from the mutation block back to the population block. It’s not there.

Differentiate between " until suitability to purpose occurs" and "reached a global maximum on the evolutionary landscape". Perhaps we are saying the same thing?

“until suitability to purpose occurs” = “purpose” (within this context) is the ability within bodily constraints to be able to kill prey effectively with no threats from them. (a global maximum on the evolutionary landscape) – there is no global maximum. Naturally, a crocodile would have a tough time killing a hippo and a shark would battle with a killer whale. These are risky and are not normal prey.

Hence...global maximum for a particular niche.

There is no global maximum. Evolution continues until the threats to survival are negligible. Then stasis.

 

[Phronesis]

A feedback loop would go from the mutation block back to the population block. It’s not there.

Why should it be there? You have a population that reproduces. The survivors are OBVIOUSLY part of the next population that reproduces (reproduction), and mutations OCCUR in that population OBVIOUSLY. No need to state the obvious, since mutations happen in reproducing populations.

“until suitability to purpose occurs” = “purpose” (within this context) is the ability within bodily constraints to be able to kill prey effectively with no threats from them. (a global maximum on the evolutionary landscape) – there is no global maximum. Naturally, a crocodile would have a tough time killing a hippo and a shark would battle with a killer whale. These are risky and are not normal prey.




There is no global maximum. Evolution continues until the threats to survival are negligible. Then stasis.

Stasis implies a global maximum for a particular evolutionary landscape. Get it?

 

[Palimino]

Why should it be there? You have a population that reproduces. The survivors are OBVIOUSLY part of the next population that reproduces (reproduction), and mutations OCCUR in that population OBVIOUSLY. No need to state the obvious, since mutations happen in reproducing populations.

Not so OBVIOUS. There is one feedback loop in the wrong place (misleading, if it’s all so OBVIOUS). This occurs between the ‘reproduction’ and ‘solution blocks’. Feedback should extend to the primary ‘population’ block (its evolution which affects the entire species (‘population’). What about the segments of the population that get killed before they can reproduce?

 

[Phronesis]

Not so OBVIOUS. There is one feedback loop in the wrong place (misleading, if it’s all so OBVIOUS). This occurs between the ‘reproduction’ and ‘solution blocks’. Feedback should extend to the primary ‘population’ block (its evolution which affects the entire species (‘population’). What about the segments of the population that get killed before they can reproduce?

The primary population is the STARTING population.

 

[Phronesis]

3'untranlated regions just junk without function? Probably not...

The Ends Of MRNAs May Prevent The Beginnings Of Cancer

ScienceDaily (Aug. 20, 2009) — The tail ends of cellular protein templates, regions often thought relatively inconsequential, may actually play a role in preventing normal cells from becoming cancerous.

The finding from scientists at Whitehead Institute for Biomedical research is reported in the August 20 edition of Cell.

Proteins are made from templates that are copied from a cell's DNA. These templates, called messenger RNAs (mRNAs), comprise three sections. The middle section codes for the actual protein, while the beginning and end sections are known as untranslated regions (UTRs) because they do not code for any portion of the protein. Instead, the beginning section gets protein production started, while the tail section, called the 3'UTR, appeared simply to be along for the ride.

"This end of the mRNA is often not considered that important because if you put the beginning and middle of the mRNA into a cell, you get the right protein," says Christine Mayr, first author of the Cell paper and a former postdoctoral researcher in the lab of Whitehead Member David Bartel. "But now we know that this end often has a protein production regulatory program and in some cases can play a role in cancer."

A cell uses proteins in almost all of its processes, from cell division, to transporting essential molecules, to providing the cell's structure. Because the cell's protein production profile is tightly controlled and specific to the cell's type and stage in its life cycle, the over- or under-production of certain proteins can alter normal cellular function. These changes can include uncontrolled cell division and the ability to grow in the absence of a substrate—both defining traits of cancer cells.

When Mayr compared mRNAs produced in normal cells with those in cancerous cells, she noticed that the tail end of the cancer cells' mRNAs were cut short. In some cases, nearly 95% of the 3'UTR was missing.

"So now, in the cancer cell, the same protein is being made, but a lot of regulatory sequences have been lost," says Mayr. "And in the beginning, I had no idea what this means. But then I found that those shorter mRNAs were making much more protein."

In fact, the shorter mRNAs were producing between two and 40 times more protein than their normal-length counterparts. When Mayr altered normal cells so they produced only shortened mRNAs for a specific gene, the cells again produced huge amounts of that mRNA's protein. And the copious proteins transformed normal cells into cancer-like cells.

"So, my theory is that in normal cells, genes are tightly regulated by their long 3'UTRs," says Mayr. "And the cancer cell somehow has the ability to express the shorter mRNA without those regulatory sequences. Without that regulation, it's able to express large quantities of protein."

Although Mayr has established a connection between short 3'UTRs and cancer cells, how the cells shorten their mRNAs remains a mystery.

"The next step is to try to explain this phenomenon mechanistically," says Bartel, who is also a professor of biology at MIT and a Howard Hughes Medical Institute investigator. "There has to be biochemical machinery that causes shortened 3'UTRs in cancer cells, something that the cancer cells have that normal cells don't have. Right now, the biochemical cause of this is not known."

David Bartel is a Member at Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a Howard Hughes Medical Institute Investigator and a professor of biology at Massachusetts Institute of Technology.

 

[Phronesis]

Just imagine if science went forward from the conclusion that:
Untranslated regions of neutral genetic junk has accumulated through evolutionary processes over the history of a genotype because natural selection rarely “trims the fat”.

Luckily science moves forward from such ill-conceieved "ideas" and delved deeper into the cause of untranscibed RNA.
Look. MicroRNAs, those small pieces of RNA that are not transcribed to proteins...

Blossoms Of Maturity: Newly Discovered Signaling Pathway Ensures That Plants Remember To Flower

ScienceDaily (Aug. 20, 2009) — Why do some plants blossom even when days are short and gray?

Scientists at the Max Planck Institute for Developmental Biology have found the answer to this question: An endogenous mechanism allows them to flower in the absence of external influences such as long days. A small piece of RNA, a so-called microRNA, has a central role in this process, as a decline of its concentration in the shoot apex triggers flowering.

MicroRNAs are very short RNA snippets that have emerged in recent years as essential regulators of gene function in both plants and animals. By binding to complementary motifs in a messenger RNA, they inhibit its translation into protein. This process thus blunts the activity of the corresponding gene.

In Tübingen, developmental biologists have discovered that the common wallcress, Arabidopsis, uses this regulatory mechanism to switch from vegetative to reproductive development. A group of related regulators, the SPL proteins, play an important role in promoting the onset of flowering. In young plants, production of SPL proteins is prevented by high levels of microRNA156.

Jia-Wei Wang and colleagues demonstrate that independent of external cues, the concentration of the microRNA declines over time, like sand running through an hourglass. When the microRNA concentration falls below a certain level, enough SPL proteins are produced to activate the flowering process even in the absence of other regulators that measure day length or external temperature. This in turns allows a sufficiently old plant to flower, even in an unfavorable environment.

Interestingly, the SPLs do double duty, since they have supporting roles when plants flower in response to long days. Furthermore, both the SPLs and other regulators eventually converge on a similar set of targets crucial for flowering.

"Flowering is crucial for the long-term survival of plants. The redundancy of environment-dependent and –independent mechanisms ensures that plants do not wait forever until flowering. Better flower once, then never," explains Detlef Weigel, director at the Max Planck Institute for Developmental Biology.

 

[rwenzori]

Just imagine if science went forward from the conclusion that:
Untranslated regions of neutral genetic junk has accumulated through evolutionary processes over the history of a genotype because natural selection rarely “trims the fat”.

What part of this quote from Wikipedia ( some quoted by cyghost above ) don't you understand?

Junk DNA is as of 2008 outdated term, being used mainly in popular science and in a colloquial way in scientific publications. Originated in evolutionary biology and molecular biology in 1972 by Susumu Ohno[1], junk DNA was a provisional label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified.

Sucking your thumb for an answer? Or is your English letting you down again?

 

[Phronesis]

Hold on, do you want to tell me this hypothesis is outdated, wrong and just a plain old lie?

The null hypothesis concerning junk DNA is that is just that: more or less neutral genetic junk that has accumulated through evolutionary processes over the history of the genotype because DNA rarely “trims the fat” so to speak.

Look at that bolded part rainman:
"for which no function has yet been identified."
Certain steroetypes latched onto this (out of ignorance) and screamed... "look, functionless junk, what a bad design if it was designed". And it goes on till this day .

 

[w1z4rd]

Originally Posted by Phronesis
Just imagine if science went forward from the conclusion that:

Got that from rwenzori`s quote. That sounds weird to me. Ive always being taught that you dont start with a conclusion and find the facts, but you let the facts lead you to a conclusion.

 

[Phronesis]

Got that from rwenzori`s quote. That sounds weird to me. Ive always being taught that you dont start with a conclusion and find the facts, but you let the facts lead you to a conclusion.

Problem is, certain people came to the conclusion the our existence must have been badly designed if it was designed (basically a massive argument from ignorance, stupid and self-refuting), and then butchered and abused science and the findings that certain parts "seem" functionless to support their idiotic preconceived conclusions.

 

[rwenzori]

Problem is, certain people came to the conclusion the our existence must have been badly designed if it was designed (basically a massive argument from ignorance, stupid and self-refuting)

Your thread is just another one of your straw men, as evidenced by the definition quoted.

In any event, your silly bit about "massive argument from ignorance, stupid and self-refuting" holds no water, and will not until the function ( if any ) is found for EVERY little tiny bit of genetic material. Maybe this will happen, maybe it won't, but as it currently stands the only ignorant illogical conclusion is your own.

You yourself are also guilty of your own accusation - "to support their idiotic preconceived conclusions". Your own idiotic preconceived conclusion is that Bebeh Jebus designed everything.

Suck it up Bebeh Jebus!

 

[Phronesis]

Your thread is just another one of your straw men, as evidenced by the definition quoted.

Answer the question rainman:

The null hypothesis concerning junk DNA is that is just that: more or less neutral genetic junk that has accumulated through evolutionary processes over the history of the genotype because DNA rarely “trims the fat” so to speak.

Is this hypothesis outdated, wrong or just a lie?

Look, we know that to come to the conclusion that our existence must have been badly designed if it was designed is just one massive argument from ignorance, it is stupid and self-refuting and there is about as much philosophical substance in that assertion as there is in the philosophy of those who think **** just happens.

 

[rwenzori]

Is this hypothesis outdated, wrong or just a lie?

Undetermined at this time, strawman.

 

[Phronesis]

Great, and the amount of useful information coming from that hypothesis is also undetermined at this time. Moving along now to something more constructive... like scientific evidence for the functions of these previously thought functionless junk...

 

[rwenzori]

Great, and and the amount of useful information coming from that hypothesis is also undetermined at this time. Moving along now to something more constructive... like scientific evidence for the functions of these previouslt thought functionless junk...

LOL! Your language does go to pieces when you're angry.

 

[Phronesis]

ROFL, moving along now...

 

[rwenzori]

ROFL, moving along now...

Hehe!