Darwin re-visited

[Buffy]

Been busy folks, but looks like you've all been having fun!

Bio has re-enunciated his front-loading hypothesis which he and I "discussed" long ago and it still presents the following dilemma for his argument:

• On the one hand, it argues for the notion that much of the genetic information in DNA has indeed been there for a long time.
• On the other hand, he insists that this information is "flat" and has no interrelationships with other parts of the genome: in other words, *all* of the variation we see must have been "front-loaded" because, in his view, there's no way to get the variation except to start over from scratch which is highly improbable.

This is the basic point I was making in my last post--and is littered among the many debates Bio and I have had in the past--that DNA is:

• Part of a system that is highly integrated into it's environment of proteins, chemical reactions, cell environments, and thus represents only part of the picture.
• An Engine for building organisms, not just a "random recipe" for a specific being.

Why is DNA so similar among widely divergent species? Because it's a well-developed mechanism for generating new ones.

In other words, it--along with *all* the stuff around it that makes it do its thing--is a Turing Machine for organisms. Slightly more complex, but amazingly straightforward in many respects.

The most important aspect of this relative to Bio's argument is that much of DNA represents "subroutines" that use "random mutation" as input. Bio has in the past argued strenuously that this is not the case, but that radical changes in DNA are required to generate the significant morphological changes that we see between species and which are necessary to explain historical events like the Cambrian explosion.

But if one recognizes the fact that change in even a *single sequence pair* in DNA can produce huge morphological changes, it becomes obvious that this "modular programming model" of evolution is well substantiated. The article "From Atoms to Traits" in the January 2009 issue of Scientific American actually has several wonderful examples of this.

In addition, DNA also contains experiments in modifications around for amazingly long periods of time, that may have been "tried" and then hidden away as recessive traits and then driven off to the misnamed "junk" DNA which become tremendously useful when environmental stresses require organisms to change rapidly or die trying. This is precisely why when the meteor hits or the supervolcano goes off, that we see *very rapid* changes in morphology, when quite frankly we see very little during more copacetic periods of history.

Why has--as Bio has often asked--there been no "evidence of speciation?" Mostly because there's no need for it at the moment. With Global Climate Change, expect so see a lot more!

But back to the issue of "complexity" which Bio brought up earlier, because it really is the crux of the issue in explaining large and rapid changes as described by Niles Eldredge and Stephen Jay Gould in their theory of Punctuated Equilibrium which Bio often uses as a "seeming contradiction" with the fact that mutations "only affect single gene pairs.

As I just stated, it's clear that DNA does indeed have an "engine" that can utilize small changes to create large morphological changes. But we need to validate this from another viewpoint that I touched upon in my previous post, which is the notion of *relationships*--or to be more specific in addressing the *statistical* argument, *dependence of variables*--between many disparate parts of DNA. mtRNA is very efficient in preventing certain changes to DNA from being instantiated, even before "selection" is required, and while there are indeed many "single pair" traits, many other traits have been described in recent genome research that include relationships between sets of genes.

When you start to try to apply a statistical argument--"the likelihood of all these changes happening in concert"--you need to recognize that these relationships as well as the fact that they exist in an environment that is hostile to certain changes while being indifferent or encouraging of others means that all statistical analysis that assumes the combination of independent probabilities is meaningless. I have tried to explain this to Bio before, but I have not gotten through, so I thought I'd try to come up with a simple, real-world example of the kind of problem this poses, that becomes unclear when people are trying to discuss already complex and hard-to-relate-to mechanisms such as DNA.

SO, join me in my little square kilometer of forest with trout stream....

I frequent a wonderful square kilometer of forest up in the Easter Sierra's that has a trout stream in it. I like to catch trout and eat them, but I have a problem. I have to find them. Consider the following data:

• The space is a square kilometer, 1000 meters on a side. My problem space includes creatures living in that space, and its reasonable that they will live no more than 10 meters underground (to bedrock) or 40 meters above ground, thus providing a 3D space of 50 million cubic meters.
• Within that square kilometer is a 1000 meter stream, averaging 1 meter across and 0.5 meters deep.
• There are 10 trout in that square kilometer.

Now I make an *outrageous* hypothesis: the trout will most likely be found in the stream.

There turn out to be two ways to compute the probabilities here:

• The independent probabilities approach says: the chances of anything in the 50 million cubic meter forest being in the 500 cubic meter stream is If we make the assumption that all probabilities are independent, then to find the likelihood that ALL 10 trout are in the stream, we multiply this probability ten times, and thus the total probability is .
• The correllated probabilities approach recognizes that trout spend about 100% of their lives in water and never get more than a 20 cm out of it jumping, usually less than 5 seconds a day (86,400 seconds). Thus the probability of the trout being somewhere out of the water is Thus the likelihood that all 10 trout are in the water is . (For the mathematically inclined, note that I've made the *mistake* here of assuming that jumping is independent, while those of us who fish know that those trout jump only during "feeding time" (usually when the mosquitoes are feeding on me!)).

While this is a different and not directly analogous example, it is exactly the trap that those who claim "high improbability" go wrong: not recognizing the interdependence of the various probabilities involved.

The point being, if you foolishly ignore the lack of independence between variables, the "virtually impossible" becomes "near certainty."

Bio, I've asked you many times in the past, but you're going to have to explain why all of the elements are independent before your reductio ad absurdum requiring an inherent design is necessary to the data we see!

Man can believe the impossible, but man can never believe the improbable,
Buffy

[HydrogenBond]

The correlation of the formation of neural memory being connected to specific adjustments at the cellular level and perhaps all the way to the DNA, via RNA, seems to indicate cause and affect relative to an environmental need. If these neural changes were random, memory would also be random. If you tried to remember a cat, random genetic integration should end up as dog, dirt, sun, moon, but it doesn't. There is a direct cause and affect between input and affect.

If we extrapolate that to an adaptation to the cold, for example, the current theory assumes a random genetic change among a group with perhaps one of the group having the correct memory. The cold affects every mind and changes the brain specifically to the memory of the affect. There is not only one critter remembering cold with the rest randomly thinking apple, orange, dirt, etc. The brain will manipulate genetics in a cause and affect way, via repeatable memory.

If you think about sex and the genitals there is both feedback and feedforward. This area of the body is rich in sensory nerves and it can also be induced into activity using sensory input or with the mind via the imagination. This suggests a broadband link between the two. Structural nervous signally (cold) is traveling down the broadband connection influencing the formation of gamete cells to influence the genetic alternation needed to deal with the original input.

“Sperm-mediated gene transfer” has been well documented by Italian researcher Corrado Spadafora [9] as a process whereby new genetic traits are transmitted to the next generation by the uptake of DNA or RNA by spermatozoa and delivered to the oocytes at fertilization. The interaction of exogenous nucleic acids with sperm cells is mediated by specific factors, among which, a reverse transcriptase that generates “retro-genes” through reverse transcription of exogenous RNA or through sequential transcription, splicing and reverse transcription of exogenous DNA. The result is to transmit low copy transcriptionally active extrachromosomal structures capable of determining new traits. Retro-genes can be further transmitted through sexual reproduction from founders to their F1 progeny as new genetic and phenotypic features, unlinked to chromosomes, and thus be generated and inherited in a non-Mendelian manner. Rare instances of retro-gene integration into the chromosome could also occur, providing further potential for evolution.

Rewriting the Genetic Text in Brain Development

The brain is the main computer of an animal. It should be able to extrapolate to what it needs to meet the stress even before it occurs. It may not have time to randomly wait for change. This transfer may not be very good in lower animals and may depend on some level of random but within a narrowing bandwidth of alternatives. Adaptation will not show a bunch of nonsense genetic changes.

[Michaelangelica]

Originally Posted by Pyrotex

i would truly hesitate to say that we are "just beginning".

I wouldn't.
I think we have just opened the door a little and peeked into a vast, richly furnished room in the Palace of Versailles. We think we know a lot because we keep making reductionist models of everything-'cause we are dumb.
EG/ie
"DNA just a binary code +2. What's the problem?"

Q1. Could Mitochondrial DNA either from mother or father(yes father) carry environmental 'Lamarking' type info?
Or to put it another way "Are the bugs/ Wee- Beastie bits we carry with us clever than us?"

Q?2. How about another "That's Funny" piece of Oz research (again) on Nano-life "Analogue DNA"?
(Thanks to Moontanman for pointing me to this)
Microscopy-UK full menu of microscopy and microscopes on the web

[Pyrotex]

Originally Posted by Galapagos

Here is a video chat from bloggingheads.tv with PZ Myers and Abagail Smith in which they discuss/explain epigentics:
Bloggingheads.tv - diavlogs

Here is a good overall summary of epigenetics from PZ Myers:
Pharyngula: Epigenetics
And Larry Moran commenting on it(good points raised here):
Sandwalk: Epigenetics

And here are more ...

Outstanding resources!! Thanks a million!
I woulda repped you if'n I coulda.

[CraigD]

Originally Posted by HydrogenBond

The correlation of the formation of neural memory being connected to specific adjustments at the cellular level and perhaps all the way to the DNA, via RNA, seems to indicate cause and affect relative to an environmental need.

This is a very strange claim, HBond! Do you have any support for it?

I’m unaware of any theory or evidence suggesting that experiences sensed and stored as memories by the nervous system can case any change whatever to ones DNA. Almost certainly, everything know about neuroanotomy and physiology indicates that changes to DNA have not role in memory, while no mechanism or evidence know to microbiology has ever shown a change to DNA as the result of experience. In short, once combined to form the nucleus of a fertilized egg, DNA appears to be purely a “read only” source of data, with the exception of damage, random transcription errors, and insertions of foreign sequences by retroviruses and other pathogens.

Originally Posted by HydrogenBond

If these neural changes were random, memory would also be random. If you tried to remember a cat, random genetic integration should end up as dog, dirt, sun, moon, but it doesn't. There is a direct cause and affect between input and affect.

Obviously, nervous systems do not form memories randomly. As noted above, however, “genetic integration” of memories is nowhere to my knowledge supported by scientific theory or evidence, but rather is pure (and rather bad) science fiction.

Again, HBond, if you know of any accepted scientific theory to the contrary, please post it. If these are purely your own ideas, however, please don’t try to pass them off as accepted science, and be prepared to either conduct original scientific research in pursuit of them, or have them considered strange claims.

[HydrogenBond]

Actually this is abased on an article that was posted by Michaelangelica that can be found at this link:

Rewriting the Genetic Text in Brain Development

The article stops short of saying the genetics in the brain cells is altered, although this seems to be what some researcher are suggesting, so it was mentioned to get the system used to the water. You know how they can get. I was suggesting the article of rewriting the genetic text in the brain shows an example, where genetic changes have a sense of direction.

At the end of the article it talks about sperm mediated gene transfer, which I never knew about but also seemed logical. The two events suggested the nervous link between the two may play a role. I also assume this occurs in forming female gamete cells since there is more time to tweak the genes needed for adaptation in the next generation.

[Moontanman]

Originally Posted by Michaelangelica

I wouldn't.
I think we have just opened the door a little and peeked into a vast, richly furnished room in the Palace of Versailles. We think we know a lot because we keep making reductionist models of everything-'cause we are dumb.
EG/ie
"DNA just a binary code +2. What's the problem?"

Q1. Could Mitochondrial DNA either from mother or father(yes father) carry environmental 'Lamarking' type info?
Or to put it another way "Are the bugs/ Wee- Beastie bits we carry with us clever than us?"

Q?2. How about another "That's Funny" piece of Oz research (again) on Nano-life "Analogue DNA"?
(Thanks to Moontanman for pointing me to this)
Microscopy-UK full menu of microscopy and microscopes on the web

Maybe nanobes need their own thread dude?

[CraigD]

Originally Posted by HydrogenBond

The correlation of the formation of neural memory being connected to specific adjustments at the cellular level and perhaps all the way to the DNA, via RNA, seems to indicate cause and affect relative to an environmental need.

Originally Posted by CraigD

This is a very strange claim, HBond! Do you have any support for it?

Originally Posted by HydrogenBond

Actually this is abased on an article that was posted by Michaelangelica that can be found at this link:

Rewriting the Genetic Text in Brain Development

Thanks, HBond! . The linked text does indeed suggest this. Another article by different authors than those reported in RtGTiBD, “RNA editing, DNA recoding and the evolution of human cognition” , speculates similarly, as do several papers linked to be these papers.

The reasoning behind this speculation seems sensible to me. Paraphrasing, it’s noted that various mechanism repair segments of DNA that are detected to have been damaged or incorrectly replicated. Some mechanisms of this kind, specifically ones related to “RNA-directed DNA repair” are known to be used in specialized cells, such as immune cells, to, rather than prevent changes to the genome, purposefully change it to cause these cells to be even more different from other cells than mechanism involving the switching off and on of genes permits. To continue with the switch analogy, rather than simply “flipping a lightswitch” to cause the cell to produce proteins coded for specific genes, this mechanism slightly rewires the lightbulb.

The various authors note that nerve cells are similar to immune cells, sharing some enzymes (Rag1 and Rag2) known to increase the number of kinds of immune cells produced by the immune system, being functionally similar in that both store information, and both using special proteins – neuroreceptors in nerve cells, identifying, signaling, and recognizing surface proteins in immune cells. It’s a reasonable step – though, as best I can read, still a guess – to speculate that DNA-altering mechanism similar to those in immune cells are used to grow and alter nerve cells.

Long-term memories – what we generally mean by “memories” – are believed with a high degree of certainty to be formed by the guided construction of new proteins in nerve cells, especially neuroreceptor proteins, and physical arrangement of nerve cells via this construction. If the construction of these proteins depends on DNA-altering, then it’s accurate to say that DNA-altering is necessary for memory formation, even though it is the arrangement of these nerve proteins, not the DNA, which actually stores the memory information.

Originally Posted by HydrogenBond

The article stops short of saying the genetics in the brain cells is altered, although this seems to be what some researcher are suggesting, …

If by “the genetics in the brain cells”, one means their DNA, then the articles are suggesting exactly that. What the primary authors stop short of suggesting, but Mae-Wan Ho, with review by Ted Steele, continue on to, is to speculate that these alterations to DNA might be passed to the next generation.

Ordinarily, alterations to somatic DNA, such as herpes virus infections, cancers, specialized immune cells, and, if the above speculation is correct, specialized nerve cells, are not passed to the organism’s children, because they don’t occur in its germline. Thus, the children of people who have had chicken pox (herpes zoster) are not born immune to contracting chicken pox, etc. Ho speculates, however, that a RNA-directed DNA altering mechanism can allow germline DNA – specifically, sperm cells – to be altered via mechanism similar to that in immune cells and nerve cells. Since this DNA uptake occurs in different places and affects functionally difference cells (sperm vs. nerve cells), I don’t see how it could transmit the “learned” DNA changes of nerve cells to subsequent generations so that, as Ho suggests, "the gains [in brain evolution] made by each generation could be accumulated."

As our ability to quickly and inexpensively sequence DNA from very small samples of cells improves, I’ll look forward to seeing confirming of refuting evidence for these speculations. We live in exciting times for biology and neuroscience.

[HydrogenBond]

I was just scanning the post in Medical sciences by NTUC about anti-psychotics. What popped into my head was a connection to the brain's manipulation of neural genetics and the neural-genetic affects associated with some mental illnesses.

One of the things mentioned was medication alone doesn't not cure the condition. It also require tweaking the DNA back (I added that) using therapy. If the memory is set up to support the genetic change. which supports it, you need to hit it from both sides or it will just regenerate itself from one side or the other.

[Symbology]

Originally Posted by Pyrotex

How many times do I have to hit you on the head with a wooden mallet before your children are born with thicker skulls?

To my observation, the interesting question is how many times do you have to hit me on the head before my offspring are born with a predisposition to dodge quicker and/or strike first and ask questions later?