Darwin re-visited

[Thunderbird]

Don't hold your breath for Lamarckism to make a comeback.

 

If you don't understand the (admittedly complex) process of DNA genetics, and the sources of genetic change, and the mechanism for sexually transmitting changes to the next generation, then Lamarckism may have a great intellectual appeal and a certain rationale.

 

However, if you DO understand those things, then you see clearly that there is NO POSSIBLE mechanism for translating an "experience" into an appropriately corresponding genetic mutation. Not even remotely, farfetchedly, conceptually, virtually possible. There is NO path, NO mechanism, NO process, NO way to translate "I almost got eaten by a new predator" into a new sequence of DNA specifically designed to provide a complex defense against that new predator.

 

Genes do NOT code for body parts. There ARE NO genes for trunks, long necks, shells, protective "caps", an extra set of pincers, eyes, teeth, fangs, claws or sacks of foul-smelling musk.

 

Genes code for proteins and enzymes. Genes code for chemistry.

 

I do not see Lamarck as opposing Darwin, or Genetic controls of Neo-Darwinism for that matter. On the contrary the conceptual ideas put forth by Lamarck are finding support among scientist recently, that my expand our models. Randomness may give way to the discovery of a secondary biochemical feedback systems on the level of a generations. If cognitive and computer memory system are divided into three stores: the sensory, the short-term, and the long-term, why not in biology ? The progress of information through these stores is often referred “The Information Processing Model”. It seems counter intuitive to conclude that DNA is a closed system and not equipped with a more complex hierarchal support system when a autonomous life is clearly embedded within one.

[Pyrotex]

...For example, selective advantage is environmental dependent. Or the environment sets the constraints of what will be an advantage. ...

Let us do a simple thought analysis. We have DNA that is 10,000 bases long. We throw the dice for 10 base pair changes in these 10,000 base pairs. I am not going to do the math but there are tons of possible ways. If purely random was in affect, we should see all of these, with very few able to actually work in terms of selective advantage..... For this to happen, the changes need to be much more targeted...

Yes, natural selection is dependent upon environment. It is the "environment" (including predators and symbiotic critters) that "perform" the natural selection.

 

Most species do not start from a few herds of identical DNA heredity. Given, oh... say, Cambodian Water Buffalo, they may all look alike, but their DNA has already accumulated millions of years worth of random mutations, most of which are relatively benign. That is, they don't kill or sicken the host--maybe they change fur color, or the thickness of the hoof, or alter the enzyme mix in the digestion, etc. See Genetic Drift.

 

My point is, the 10 changes to 10,000 base pairs, and the lottery, examples do not mirror the real problem in Nature. Let's start again with a real problem, a herd of 10,000 nearly identical water buffalo (WB), rather than a single abstract chain of DNA. After all, we rarely see chains of DNA wandering around. ;)

 

Those WB already contain millions of benign differences in their DNA. Every sexual mating takes a random sample from male and female and produce a new, unique, combination of genetic properties. Let's say the environment has lots of rivers, just the way WB like it. So, this benign mutation for thicker hooves offers neither a selective advantage nor a disadvantage. It has achieved equilibrium in the population--say, maybe 15% of the animals carry the gene. It may have been in the species for 10 million years.

 

Climate changes and the rivers start drying up in the summers. WB with the "thick hoof" gene have a slight advantage in this new environment. The gene spreads through subsequent generations, altering the shape and form of the WB. Notice that we do NOT have to wait for a good mutation to save the WB!! Evolutionary change in the WB begins immediately!!

 

So, we don't have to speak of lotteries, or calculate the odds that 10 random DNA changes will do this or that. Those WB already carry millions or billions of "random" or "quasi-random" or "selected for" variations in their DNA--variations that are just sitting there doing no harm and little if any good--just waiting and waiting and waiting for the environmental pressures to shift.

 

So, even if only one mutation in a million is good, or at least benign, millions of mutations will occur in the herd every generation. Maybe one mutation will be benign enough to "accumulate" in the gene pool every year. Over millions of years, it's not difficult to see that an astronomical library of potential changes will accumulate, mostly just sitting there waiting.

 

It's not the probability of one mutation being "good" that matters.

 

It's the eventual and inevitable accumulation of mutations that aren't "bad" that matters.

[Pyrotex]

...If cognitive and computer memory system are divided into three stores: the sensory, the short-term, and the long-term, why not in biology ? ....

Because it doesn't.

All you have to do is observe the nature of DNA and the processes that build it and read it to see that it does not work like a freakin' computer with RAM and a processor and ethernet cables.

 

It is up to YOU to provide a mechanism for an experiential event in an animal's life, oh... say, having to stretch its neck further and further every year to reach the leaves in acacia trees... provide a genetic mechanism to:

1> identify a "stress" in the animal's life that could be "cured" by a modification of body shape;

2> translate this "stress" on the animal into a "proto-genetic command" for longer necks;

3> feed this command into a "computer" that computes a new sequence of DNA base pairs that would

4> intentionally produce an altered set of proteins in the embryo, which would

5> intentionally alter the size of the animal's neck bones as it grows to gestation and beyond; and then

6> "insert" this new DNA sequence (replacing the older sequence) into either ovum or sperm cells, so that the consequence of the "stress" eventually yields progeny with longer necks.

 

Step #2 is the Killer. You must go from some biological symbol for a specific kind of stress (food almost out of reach) and compute through the following steps: calculating a solution (need longer neck), calculating what proteins will produce that solution, calculating what base-pairs will produce those proteins, calculating where in the DNA to insert those base-pairs, calculating at what point in the development of the zygote that the new DNA needs to be expressed -- ALL BEFORE you actually generate a genetic change that eventually leads to the first giraffe.

 

Don't wave your hands and talk to me of the "information model".

Tell me how DNA or RNA is going to perform the multi-stage calculation to accomplish steps 2, 3, 4 and 5.

 

Besides which, Random Genetic Change, Genetic Variation through Sexual Reproduction and Natural Selection already already already already form a totally complete solution to the problem. You don't need the "information model".

[Pyrotex]

I'm able to see several possible ways to do this (I guess this means I must not understand genetics?). For instance, UV light causes TT dimers to form in DNA (look up "pyrimidine dimers" on wikipedia to learn more). ...

Sorry, but unless I'm mistaken, you're answering a completely different question.

Sure, UV can cause DNA damage. That is NOT the issue here.

Lamarckism is the theory that "experiential stress" can cause a "directed" change to DNA.

 

For example, can soaking potatoes in cold water before planting cause them to sprout earlier in the growing season? And will this new property breed true?

 

Lamarck himself attempted this experiment and thought that it worked! It doesn't.

 

Can the appearance of a new predator give rise to a new mutation specifically directed at providing protection from the predator in the next generation? No.

 

Will intensive body-building over many years (like Arnold did) not only change your body shape, but also cause a genetic tendency for your children to be born with that new body shape? No.

 

See the difference?

[Thunderbird]

Epigenetic Gene expression over a short time would enviably lead to long term morphological expression. If Epigenetic expression is based on stressors like say.. a lack of nutrients because leaves in an area are to high for a short necked antelope the stressed animal will pass on these traits to its immediate offspring. The animals that received a bit more nutrients by being taller will not pass on these defective traits. Epigenetic Gene expression culls the herd of shorter necks in short order.

 

see Epigenesis (biology).

In biology, the term epigenetics refers to heritable changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence (hence the name epi - "in addition to" - genetics). These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism;[1] instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently.[2] The best example of epigenetic changes in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo which in turn become fully differentiated cells. In other words, a single fertilized egg cell - the zygote - changes into the many cell types including neurons, muscle cells, epithelium, blood vessels et cetera as it continues to divide. It does so by activating some genes while inhibiting others.[3]

[Pyrotex]

Epigenetic Gene expression over a short time would enviably lead to long term morphological expression. If Epigenetic expression is based on stressors like say.. a lack of nutrients because leaves in an area are to high for a short necked antelope the stressed animal will pass on these traits to its immediate offspring. The animals that received a bit more nutrients by being taller will not pass on these defective traits. Epigenetic Gene expression culls the herd of shorter necks in short order.

Why wouldn't malnutrition cull the herd just as well? ;)

[Thunderbird]

Why wouldn't malnutrition cull the herd just as well? :naughty:

 

I do not have a good answer for that. Being a systems thinker I just tend to lean toward any evidence that suggest a higher connectivity rather than less.

[Pyrotex]

Being a Systems Thinker, I tend to lean toward Occam's Razor. The simplest explanation that requires the fewest assumptions is probably the best explanation.

[Thunderbird]

Being a Systems Thinker, I tend to lean toward Occam's Razor. The simplest explanation that requires the fewest assumptions is probably the best explanation.

Occam's Razor works quite well within epigenetic research. It is based on data not assumtions.

[Galapagos]

Well, not really. I have worked on this post for over 2 hours, and I don't think it is particularly clear. But let me give it a shot....

 

I appreciate you finally citing your claims, and it would seem as though you have backed off of your claims about PE/Cambrian being "at odds with speciation-by-mutation", and Junk DNA being "front/pre loaded" in a way that implies an Intelligent Designer. I'm glad the discussion has been able to progress, and there may be some interesting points of discussion(some I might agree with, some I may not) in the post quoted above, but first, it isn't clear where you disagree with this:

Mutation | Learn Science at Scitable

[Galapagos]

That might be what evolutionary biologists mean, but why would they say this as though it distinguishes mutation from natural selection? Scientists generally make the metaphysical assumption that the future does not cause the present, i.e., events are not caused by their consequences; processes do not take place because of their outcomes. This is fundamental to mechanistic thinking. Presumably every scientist believes that every natural process is "random" in the sense of "not goal-directed, not moving with a purpose toward a goal". Instead of saying "mutation is random", they should be saying "evolution is random" meaning "evolution is not goal-directed, not moving with a purpose toward a goal".

 

I suspect part of the reason the language ended up like this was to distinguish Darwinian evolution from competing ideas like mutationism and Lamarckism before the firm establishment of the MS.

 

I agree that it can be confusing, and I think some evolutionary biologists recognize this as well. The best explanation of random mutation that I think I've read was in R Dawkins' "The Blind Watchmaker":

The first respect in which mutation is non-random is this. Mutations are caused by definite physical events; they don't just spontaneously happen. They are induced by so-called 'mutagens' (dangerous because they often start cancers): X-rays, cosmic rays, radioactive substances, various chemicals, and even other genes called 'mutator genes'. Second, not all genes in any species are equally likely to mutate. Every locus on the chromosomes has its own characteristic mutation rate. For instance, the rate at which mutation creates the gene for the disease Huntington's chorea (similar to St Vitus's Dance), which kills people in early middle age, is about 1 in 200,000. The corresponding rate for achondroplasia (the familiar dwarf syndrome, characteristic of basset hounds and dachsunds, in which the arms and legs are too short for the body) is about 10 times as high. These rates are measured under normal conditions. If mutagens like X-rays are present, all normal mutation rates are boosted. Some parts of the chromosome are so-called 'hot spots' with a high turnover of genes, a locally very high mutation rate.

 

Third, at each locus on the chromosomes, whether it is a hot spot or not, mutations in certain directions can be more likely than mutations in the reverse direction. This gives rise to the phenomenon known as 'mutation pressure' which can have evolutionary consequences. Even if, for instance, two forms of the haemoglobin molecule. Form 1 and Form 2, are selectively neutral in the sense that both are equally good at carrying oxygen in the blood, it could still be that mutations from 1 to 2 are commoner than reverse mutations from 2 to 1. In this case, mutation pressure will tend to make Form 2 commoner than Form 1. Mutation pressure is said to be zero at a given chromosomal locus, if the forward mutation rate at that locus is exactly balanced by the backward mutation rate.

 

We can now see that the question of whether mutation is really random is not a trivial question. Its answer depends on what we understand random to mean. If you take 'random mutation' to mean that mutations are not influenced by external events, then X-rays disprove the contention that mutation is random. If you think 'random mutation' implies that all genes are equally likely to mutate, then hot spots show that mutation is not random. If you think 'random mutation' implies that at all chromosomal loci the mutation pressure is zero, then once again mutation is not random. It is only if you define 'random' as meaning 'no general bias towards bodily improvement' that mutation is truly random. All three of the kinds of real nonrandomness we have considered are powerless to move evolution in the direction of adaptive improvement as opposed to any other (functionally) 'random' direction. There is a fourth kind of non-randomness, of which this is also true but slightly less obviously so. It will be necessary to spend a little time on this because it is still muddling even some modern biologists. (...)

He then goes on to explain the fourth way in which mutation is constrained or not random, which would be a lack of genetic opportunity(he uses the example of why bats haven't sprouted arms/wings like angels; selection certainly would have taken advantage of such an opportunity, but such a mutation probably never arose).

He states "no general bias towards bodily improvement", and this is the point, as you have noted. Natural selection makes the necessary connection between organism and environment; with respect to the immediate problems faced by a population, mutations are random.

[dabs]

Sorry, but unless I'm mistaken, you're answering a completely different question.

Sure, UV can cause DNA damage. That is NOT the issue here.

Lamarckism is the theory that "experiential stress" can cause a "directed" change to DNA.

 

For example, can soaking potatoes in cold water before planting cause them to sprout earlier in the growing season? And will this new property breed true?

 

Lamarck himself attempted this experiment and thought that it worked! It doesn't.

 

Can the appearance of a new predator give rise to a new mutation specifically directed at providing protection from the predator in the next generation? No.

 

Will intensive body-building over many years (like Arnold did) not only change your body shape, but also cause a genetic tendency for your children to be born with that new body shape? No.

 

See the difference?

 

No. Previously you asserted it was mechanistically impossible that an experience should lead to mutations that improve fitness, and that someone with a knowledge of genetics would see that. The words used in a previous post were "Not even remotely, farfetchedly, conceptually, virtually possible." which (I think its fair to say) is an unconditional assertion of impossibility. I disagree, so I used my knowledge of genetics to imagine a possible mechanism by which an experience would lead to mutations that tend to be beneficial in relation to that experience. In my example, the external condition is UV light, and the outcome is a tendency for mutations that reduce susceptibility to damage by UV light. More specifically, exposure of an organism to UV light tends to cause damage at TT patterns in the DNA, and this, in turn, tends to produce mutations away from TT, reducing the TT frequency in the genome.

 

Notice that my example is not in terms of big furry animals, but thats all right because you said this was impossible therefore any example will suffice, whether or not it involves water buffalos. Notice also that I am invoking a statistical tendency, not a certainty. Insisting on certainty would make the question uninteresting. Generally in science we allow that causes can act in a probabilistic context, e..g, selection does not produce certainty either, but produces merely tendencies.

[HydrogenBond]

If we take a plant with a given DNA, and subject it to different environments, we can get a variety of growth habits. The plant will not change species, since that is defined by the DNA. But the DNA can be triggered in various ways in terms of the activity of particular genes. The plant's DNA reacts to the environmental feedback to form a growth habit that is defined by the DNA in the context of the environment. Anyone with a black thumb knows even hybrid seeds with the best DNA does not guarantee success. Controlling the environment is just as important to get the most out of the DNA.

 

Say we added a new stress the plant has never saw before. There is nothing on the DNA to respond in an exact way. Based on the above, if there was a gene, it would become more active due to that known stress. But without the needed gene, there should still be feedback to the DNA, but no good place on the DNA for an exact correspondence. There should still be hot spots on the DNA, but without perfect correspondence. The question is, do these hot spots have a greater tendency to mutate?

 

Galapagos pointed out that not all genes have the same likelihood to mutate. Some areas are hotter than others. If you look in terms of an energy balance, defects in base pairing means higher energy, which corresponds to hot spots that become built into the structure. One may call that coincidence, but the energy adds up. The cause and affect between the environmental potential and the DNA targets areas mostly likely to give beneficial change because there is already a loose correspondence. The cell needs a gene to make a protein that can deal with the stress. Point B is already defined in terms of the goal.

 

A loose analogy analogy is, the boss gives you a routine task. You follow a procedure and get it done quickly. If he gives you something new where the routine procedures break down, the task sets the goal for a new procedure. You don't just randomly look at broccoli if the goal is chicken. The hot spots will be similar to other chicken procedures but will need to be tweaked. The hot spots are the closest match and will therefore require the least amount of random change. Too much random is a waste of time and energy.

[Michaelangelica]

For- ish Lamark

Now all that is changing. No one is arguing that Lamarck got everything right, but over the past decade it has become increasingly clear that environmental factors, such as diet or stress, can have biological consequences that are transmitted to offspring without a single change to gene sequences taking place.

Rewriting Darwin: The new non-genetic inheritance - life - 09 July 2008 - New Scientist

Agin

Genomicron: Epigenetics and Neo-(Neo-)Lamarckism.

Sandwalk: 07/01/2008 - 08/01/2008

 

PS

Added link

"When most biologists hear the name Lamarck or the term soft inheritance, the reaction is, 'Oh my God, here we go again',"

Richards says. "But from a molecular biology point of view there is a mechanism to do soft inheritance, and epigenetic inheritance can be construed as a form of soft inheritance.

That's all I'm saying. The really heretical thing to say is that the environment could be pushing the epigenetic information in a direction that is beneficial. This is the more extreme variation of soft inheritance that raises the hackles."

 

Packing DNA

 

Epigenetic mechanisms leave DNA sequence unaltered but can affect DNA by preventing the expression of genes. Richards cites a study that shows certain epigenetic alleles can be inherited that affect tumor suppressor genes. His own work in plants has often shown epigenetic information can be inherited.

The Richards lab specializes in epigenetics, a biological field that deals with information stored "above and beyond the gene," referring to the Greek meaning of the term. A classic epigenetic mechanism is a process known as DNA methylation, a chemical modification of cytosine, one of the four chemical subunits of DNA.

Without proper DNA methylation, higher organisms from plants to humans have a host of developmental problems, from dwarfing in plants to certain death in mice.

http://www.sciencedaily.com/releases/2006/08/060807154715.htm

[Pyrotex]

No. Previously you asserted it was mechanistically impossible that an experience should lead to mutations that improve fitness....

I am quite at a loss to understand how you could misunderstand my response to your post. :hihi:

 

UV light causing a mutation is DIRECT damage to DNA. It is a DIRECT CHANGE to DNA.

 

An "experience" does NOT include direct damage to DNA. An "experience" is like, oh, say, building up your muscles, or going on a vegan diet, or learning French, or changing religions, or walking more on weekends. These things do NOT in and of themselves cause DIRECT changes to DNA. they only cause changes to the "phenotype"--to the physical body or to behavior or both.

 

There is nothing I've read of, including epigenetics, that can "detect" an "experience" and translate it into a change in DNA.

[Michaelangelica]

Here is a collection of noted biologists commenting on the next 200 years of Evolutionary Theory.

I found them VERY disapointing overall

 

Am I being too harsh?

What do you think of the comments ?

Any favourites?

 

This one I thought the most interesting and thought provoking.

Stuart Kauffman

 

Darwin changed our thinking as much as any scientist. Life, as zoologist Ernst Mayr said, only makes sense in terms of evolution. But major issues arise, such as the fact that Darwin did not know about self-organisation. Abundant work over the past four decades has begun to show that self-organisation plays a role along with natural selection in the order in biology. One example is that lipids spontaneously form liposomes, the hollow bilayered vesicles that must have yielded the cell membrane. Another is the spontaneous order in genetic regulatory networks, the understanding of which may lead to regenerative medicine and new cancer therapies.

 

Stuart Kauffman is professor of biological sciences at the University of Calgary, Alberta, Canada

Evolution: The next 200 years - life - 28 January 2009 - New Scientist

[Michaelangelica]

Interesting article, throwing another level of complexity into the evolution process.

It fried my brain a little

I still want to know who or what decides to make these changes.

Rewriting the Genetic Text in Human Brain Development

 

How adaptive epigenetic changes that can rewrite genes contribute to human brain development and evolution Dr. Mae-Wan Ho

 

 

An electronic version of the full report can be downloaded from the ISIS online store. Download Now

Rainbow and the Worm, 3rd Edition What makes brainy primates?

 

The brains of higher animals become increasingly complex in the course of evolution, reaching a pinnacle in primates and the human species.

And among the most tantalizing discoveries since the sequencing of the human and other genomes are the genetic and epigenetic events associated with the evolution and development of the human brain.

Rewriting the Genetic Text in Brain Development