Darwin re-visited

[Moontanman]

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]

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?

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! :shrug:. 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.

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]

 

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?

[Symbology]

...We are just beginning to understand the decryption of the DNA at this point. Due to our ability to encrypt knowledge, I would not be surprised to find out that Nature has had us beaten on the subject for a few billion years.

i would truly hesitate to say that we are "just beginning". This gives the impression that what little we know NOW is insignificant and unreliable. That is not the case. We know an astounding amount of knowledge about DNA and its decryption processes. Certainly we do not know everything, but what we have now serves to explain so much, that we now wield that knowledge in new medical applications every year.

 

First, I should explain that what I meant was not our decryption of DNA, but the cell's decryption of DNA. But our understanding of both is relatively in the same state.

 

I think at some point in the future, we will know everything there is to know about DNA, and will move on to more difficult problems. And when we do, I think they will look back at the last 100 or so years and consider it as covering important ground, but still only scratching the surface.

 

There is still so much that we don't understand about protein folding, cassette mutation, and the quantum computing that goes on within enzymes etc.

 

We have a beginning map similar to what we have of the brain right now. We know if we put an electrode to a certain part X of the brain that this part Y of the body twitches. But we still have a huge amount to go in understanding the phased brain wave patterns, connections, electro-chemical washes, etc. We have a decent amount of knowledge about the brain's structure, but not it's micro level behavior.

 

And similarly we have a decent amount of knowledge about DNA's structure, but so much more to go relative to it's behavior in concert with RNA and enzymes during it's normal processing.

[Pyrotex]

...Epigenetics does not equal experiential evolution.

I agree with that statement. However, I think the idea was proffered somewhere in this thread that if Lamarkian genetics had any plausibility, it might be mediated via epigenetics. Lamarkism IS experiential evolution. Reach really hard for those high branches and your children will be born with longer necks.

 

I have done some reading on epigenetics since then, and what I can find says that epigenetics in one sense, is the ability of the female reproductive system to generate chemical messengers that can selectively turn on or turn off specific, well-established, genetic sequences in the fetal DNA. Primarily, this is done as a well-defined time sequence of zygote development.

 

In a second sense, this also includes the ability to detect and turn off sequences of DNA that have been damaged beyond repair. In a third sense, epigenetics is a "grab bag" of processes that could conditionally enable or disable DNA sequences, even in such a way that the change could be passed on to the subsequent generations.

 

I believe it was this final "definition" of epigenetics that some are claiming is the machinery of Lamarkian (experiential) genetics. An interesting concept, but as I have noted before, the idea has a flaw that I believe is fatal.

[Michaelangelica]

This evolution caper is complex. here is some more stuff to stir the pot.

 

Any comment on nano DNA analogues yet?

 

How?

Who or what decides?

The organism?

The environment?

x ?

"We are finding that today's complicated vertebrate has not invented a lot of new genes to become complicated," she said.

"Amphioxus shows us that vertebrates have taken old genes and recombined them, changed their regulation and perhaps changed the gene function."

 

Such duplication has given humans and other vertebrates a much larger "toolkit" for making various structures that are absent in amphioxus, including cells for pigment and collagen type II-based cartilage, for example.

 

Putnam noted another interesting finding reinforced by the amphioxus genome: Most creatures have a lot more genetic variation than humans. While two humans typically differ at only one nucleic acid per thousand in the genome, two lancelets differ at one of every 16 nucleic acids.

 

"Marine invertebrates actually vary about 6 percent, which means that, on average, one of every 16 bases is different, which is pretty remarkable - it's the difference between humans and certain types of apes," Putnam said. "Humans really are a special case, because of the recent out-of-Africa bottleneck and because of the size of our population. There is a lot less variation than in these little wormy guys that live by the millions in shallow water."

University of California - UC Newsroom | Lancelet genome shows how genes quadrupled during vertebrate evolution

The neural crest cells of vertebrates are an excellent example of how “old” genes have acquired new functions. In all vertebrates, neural crest cells migrate from the developing neural tube throughout the body, giving rise to such structures as pigment cells, cartilage of the head and a number of other cell types.

Although amphioxus has a brain and spinal cord and makes them using the same genes in the same way as vertebrates, amphioxus has no neural crest cells.

Even so, amphioxus has all of the genes necessary for generating migratory neural crest cells; vertebrates have just put them together in new ways. It can be compared with a chef who takes basic leftovers in a refrigerator and whips up a fine gourmet dish.

“The take-home message from this sequencing is that the human and amphioxus genomes are very much alike,” said Holland.

Worm-like Marine Animal Providing Fresh Clues About Human Evolution

Our brother/sister

Duplicates of developmental genes were preferentially retained. Although some genes apparently acquired roles in neural crest prior to these genome duplications, other key genes (e.g., FoxD3 in neural crest and Wnt1 at the MHB) were recruited into the respective gene networks after one or both genome duplications, suggesting that such an expansion of the genetic toolkit was critical for the evolution of these structures.

.. .

Thus, vertebrates have a much larger number of proteins available for mediating new functions in these tissues. The creation of new splice forms typically changes protein structure more than evolution of the protein after gene duplication.

Gene Duplication, Co-Option and Recruitment during the Origin of the Vertebrate Brain from the Invertebrate Chordate Brain

 

 

The amphioxus song “Its a long way from amphioxus”

PubMed Central, Figure 3: Int J Biol Sci. 2006; 2(2): 30?31. Published online 2006 April 10.

[Pyrotex]

Happy 200th Birthday, Charles Darwin!!!

 

:happybirthday: :bdayparty: :bouquet:

:) :bdayparty: :bouquet: :happybirthday:

:bdayparty: :bouquet: :happybirthday: :)

:bouquet: :happybirthday: :bdayhappy_balloons: :bdayparty:

 

...and of course...

[HydrogenBond]

I have been thinking about why I can't just accept the current version of evolutionary theory, as is. I think I have my gut figured out. It has to do with curve fitting of data. Evolution, in my mind, extends from the zero point, where life begins with simple chemicals such as methane, ammonia, etc.

 

Darwin's origin of species, was concerned with the subset of data called species. His theory drew the best curve through the subset of evolutionary data called species data. The analogy is say we data plotted all of evolution, along an x-axis from 0 to 100, Darwin drew the best curve using the data from 50-100. This curve may not be the same curve as the one that uses all the data from 0-100. This turned out to be the case.

 

After Darwin, microscopic life data was added to the macroscopic data of Darwin. This required the genetic addendum to the original Darwin theory so the new curve would be the best fit of the data, but with the curve fitting the data from 20-100. Once more data was added the curved needed to be modified.

 

In my mind, although the data 0-20 is not easy to come by, the final evolutionary curve needs to include this extra data, with the curve needing to touch the origin at 0, or else, the curve could be hanging in space and could be transposed vertically. I have no problem with the fact the current version of evolution fits the data from 20-100. But it does not touch the origin, although it might extend to replicators at about 10.

 

The way I look at it, whatever fits the curve from 0-20 sets the original pattern for evolution. It would be the addendum to genetics just as genetics was the addendum to Darwin. I assume there has to be something even more fundamental than genetics which is needed to make it touch the origin.

 

The places I looked has to do with water and hydrogen bonding. Water is the majority component of life and hydrogen bonding is an active variable that the organics and water have in common. It appeared to be the most logical way for the organics to integrate with the majority component. This premise can address 0-20 or how the organics are expected to act in water. It is hard to overcome the best fit from 20-100, because it is philosophically assumed to be the best fit from 0-100, without the requirement it needs to touch the origin.

 

Let me give a practical example of where the fit from 0-100 will still work, but where the fit from 20-100 can have problems. Say the new selective advantage of a species comes from a new behavior, such as crawling under leaves as a way to survive in the cold. This does not have to have a genetic origin, but can originate with the brain and some trial and error. Eventually this behavior may become part of the species that survives the winter and become engrained into genetics so the offspring do this by instinct.

 

From the point of view of water and hydrogen bonding it doesn't matter what direction the genetic change occurs as long as it defines equilibrium. The imbalance between genetics and altered behavior, can either make him leave the leave pile to stay true to genetic based behavior, or it can alter the genetics to the necessity, with altering the genetics offering more selective advantage.

 

This may seem far fetched, but it has been proven the brain can alter the mRNA that is coming off the DNA. In the example above, the cause is the memory of crawling under the leaves and the survival advantage that the entire body will feel. The affect is the genetic tweak which is an equilibrium affect. The animal does not have to wait for a random change or have to use something already in the DNA, but can get more out of the DNA than is on the DNA, in the traditional sense of 1 gene = 1 protein. It turns out 1 gene can make more than one protein, to order, at least in the brain and immune system. These two tissues just so happen to be everywhere throughout the animal body along with the circulatory tissue. An equilibrium analysis doesn't have an problem with this. But it does not fit into the curve from 20-100.

[Symbology]

Hydro,

 

Carl Sagan did a blurb on The Primordial Soup some 20ish years ago. It basically covers the transition from 0-20 that you are talking about. Wiki has a write up here.

[HydrogenBond]

I understand the organic aspects of life have been looked into, because the organic products are the building blocks of life. But the question I asked. that is not addressed, is why life molecules use the hydrogen bonding feature that is also common to water? This is a basic observation and will occur as the final result, no matter which mechanism or theory one prefers to use. All theoretical roads lead to this same end, yet I didn't read anything that stresses this basic observation. All the models imply in water, but water and hydrogen bonding is not included in the analysis since the theory is more concerned with the covalent bonding of molecules.

 

If you look at a protein it is a long covalent polymer. But its life properties are dependent on the secondary, tertiary and quaternary shapes it forms that are held together by weak secondary forces, the most important of which is hydrogen bonding. The final shape is also dependent on assuming a configuration based on aqueous considerations. This is where life properties are added to a polymer that would be inert in any other solvent other than water.

 

Even the DNA double helix has a double helix of water built in. The evolution of the DNA is the evolution of this quadruple helix of water and DNA, but the water is assumed invisible within abiogenesis models. I am not the one leaving out variables.

[CraigD]

I understand the organic aspects of life have been looked into, because the organic products are the building blocks of life. But the question I asked. that is not addressed, is why life molecules use the hydrogen bonding feature that is also common to water?

Asking why an chemical mechanism, “life” or of some other category, “uses” the properties of its chemical agents strikes me as a strange question, carrying with it the implication that these agents have some sort of free will and choice over how they behave. It’s answer requires the rejection of this implication, I think, and is “because they must behave according to their properties.”

This is a basic observation and will occur as the final result, no matter which mechanism or theory one prefers to use. All theoretical roads lead to this same end, yet I didn't read anything that stresses this basic observation. All the models imply in water, but water and hydrogen bonding is not included in the analysis since the theory is more concerned with the covalent bonding of molecules.

In a few minutes, starting with a google search of nonaqueous protein, I read several abstracts and texts observing the importance of water to protein folding and function, and the behavior of protein in less aqueous solvents.

 

Describing the observation that water is important to biochemistry as “the final result” strikes me as strange. I would describe this observation as preliminary.

 

If you look at a protein it is a long covalent polymer. But its life properties are dependent on the secondary, tertiary and quaternary shapes it forms that are held together by weak secondary forces, the most important of which is hydrogen bonding.

While hydrogen bonds have long been know to be very important to protein folding, labeling them “the most important” to the exclusion of other mechanisms is, I think, inaccurate. Bonds between other atoms in proteins are also very important.

 

Protein folding is very complicated, and far from well understood. HydrogenBond is accurate, I believe, in noting that most of the many scientists working in the field adhere to a “central dogma” that the sequence of amino acids in the linear chain of a protein are most important in determining its folded structure, but incorrect in his claim that they completely ignore other factors, such as the role of the solution in which proteins form, and the role of water and other molecules in this solution.

 

This is where life properties are added to a polymer that would be inert in any other solvent other than water.

Proteins are not inert in solvents other than water, as stated in numerous sources, such as

Enzymes are capable of catalysing reactions in organic or non-aqueous solvents, being this feature, besides its scientific interest, of fundamental importance in biotechnology. However, the knowledge of protein structure and dynamics in these type of media is limited. Most of the knowledge is about proteins in aqueous solvents.

, from Understanding protein structure and enzyme kinetics in non-aqueous solvents — ITQB, the third result of the search described earlier in this post.

Even the DNA double helix has a double helix of water built in. The evolution of the DNA is the evolution of this quadruple helix of water and DNA, but the water is assumed invisible within abiogenesis models. I am not the one leaving out variables.

In most biochemical settings, water is a liquid, so it can’t have a crystalline structure such as a double helix. It’s molecule is also many times smaller than any dimension of a molecule of DNA, so if we were to consider some arrangement of water around DNA to be a “built in” double helix, there would be more than just one possible.

 

Due to its lack of crystalline structure, information can’t be stored in useful way in liquid water, the way it’s stored in DNA. Without the ability to store information, it can’t transmit heritable traits between generations. So, despite its importance to life and the biochemistry of DNA, heritance, and evolution, water can no more be said to “evolve” than atmospheric oxygen, which is also important to life, can.

 

Therefore, I believe people modeling biochemical processes and theorizing about the origin of life are justified in focusing their attention on molecules that can store information, such as RNA and DNA.

[Pyrotex]

I understand the organic aspects of life have been looked into, because the organic products are the building blocks of life. ... I am not the one leaving out variables.

Hello, HBond

there are variables and there are variables.

 

I have to admit, you are one of the most verbally adept and well-educated evolution skeptics I have seen around these parts. My hat is off to you.

 

But, frankly, I don't believe it's the "variables" that are bothering you.

I appreciate your reluctance to accept evolution, but its validity is not going to be proven or disproven by burrowing waaaaay down into nitty-gritty details of water bonding in chemical reactions that take place in some teensy aspect of DNA that we have only recently discovered and still do not fully understand--or in some as yet hypothetical bridge between non-living and "living" molecular systems that occurred around 4 billion years ago.

 

It's like saying that the internal combustion engine could never power an automobile because in the combustion of simple straight chain hydrocarbons in a piston, we will never understand exactly how each combustion product is formed, in what order, and how fast. Those are details far far far removed from the validity of the principal itself. And those details don't have to be answered to everyone's satisfaction in order to demonstrate that an automobile works.

 

Or, it's like saying that the internal combustion engine could never power an automobile because you can prove that it could never reach speeds in excess of Mach 1. Well, speeds that high aren't necessary. If the internal combustion engine can reach speeds of 25 MPH, you got an automobile.

 

And finally, why would you look in your "gut" for an explanation of you reluctance? Isn't "gut" a euphemism for emotions?

[Moontanman]

HB, water is nothing but the grease in the mechanical apparatus of life. I am quite sure we will eventually find other lubricants that work just as well and maybe even better.

[Michaelangelica]

Wouldn't old Mr D love to be alive today.

I wish I was a biologist.

Can we crack cancer in 20 years?-- aging in 40?

This would leave him gob-smacked -as it does me.

The discovery of P elements

 

listen now | download audio

 

Stuart Gilchrist describes the role played by fruit flies in the discovery of P elements. P elements are sections of DNA which have become a universal tool of molecular biology. They have provided the tool used to clone most animal genes during the last 15 years. The story is linked to the proliferation of human transport and trade.

 

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Transcript

 

Robyn Williams: Charles Darwin of course hadn't heard of genetics or genes, which makes his intellectual feat all the more formidable, having to imagine what might be there in you and me and beetles and flies, making it all happen.

 

And when genetics did take off, bang, at the start of the 20th century, people quickly got most of it worked out. Or did they? How come there are still huge surprises in the post-Darwinian world? Stuart Gilchrist is at the University of Sydney.

 

Stuart Gilchrist: Despite global financial turmoil, it's still easier to pick winners in the stock market than to predict winners in science. It is almost impossible to know whether basic research will lead to great advances in the future or merely end up in the dustbin of history. Even the venerable Isaac Newton spent more time studying alchemy and magic than he did studying physics or calculus. One could argue that at least half of current university research will turn out to have been pretty much a waste of time. The trouble is we don't know which half.

The discovery of P elements - Science Show - 7 February 2009

 

I just started reading Mr. Darwin's Shooter. Beautifully written and that's where I am going now to read some more.

[Michaelangelica]

An intersting couple of comments I thought.

 

"All our microscopes are customised for life as we know it - so it's no surprise that we haven't found microbes with different biochemistry," said Professor Davies.

. . .

we must begin trawling the world's most inhospitable environments - deserts, salt lakes, and areas of high pressure, temperature or UV radiation.

 

"We could have a 'mission to Earth'. There's a big long list of places we could be looking," observed Professor Davies.

 

"For example, if we are looking for arsenic life, we could head for environments which are both arsenic rich and phosphorus poor - such as deep ocean vents.

. . .

 

 

"The accepted definition of life is a molecule capable of Darwinian evolution, so we are trying to put together molecules that are capable of doing it."

 

But he questioned whether our definition of "living" is perhaps too "Earth-centric".

 

"Remember - just because you are a chemical system which is self-sustaining and capable of Darwinian evolution, that doesn't mean that is the universal definition of life," he said.

http://news.bbc.co.uk/2/hi/science/nature/7893414.stm

[Symbology]

Stuart Gilchrist: Despite global financial turmoil, it's still easier to pick winners in the stock market than to predict winners in science. It is almost impossible to know whether basic research will lead to great advances in the future or merely end up in the dustbin of history. Even the venerable Isaac Newton spent more time studying alchemy and magic than he did studying physics or calculus. One could argue that at least half of current university research will turn out to have been pretty much a waste of time. The trouble is we don't know which half.

 

I'm guessing that if scientists were held to the same scrutiny as a publicly traded company, and required to file full disclosure financial... er research sheets - that we would also be able to predict who the winners and losers would be with equal ability. But until scientists start getting funded like corporations and their accounting departments, then I'm afraid Mr. Gilchrist is correct :)