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Darwin re-visited


Michaelangelica

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Here are his criticisms of two aspects of Darwin's theory.

http://www.post-gazette.com/pg/06149/694046-85.stm

The above is an extensive quote from a Dr Schwartz. What I find surprsing is that there is nothing in the quotes that does not match my understanding of the current status of evolutionary theory. Nothing he says is new. Nothing he says is a challenge to the Modern Synthesis of Darwinism, that has been around for half a century. Except, perhapsm the remarks on gradualism, that were well tackled by Gould and his punctuated equilibrium, by the early 1970s.

I think you need to bring yourself up to date. No offense intended. Your objections are all seemingly valid, it is just that I think they have all been dealt with over the last sixty or seventy years.

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Perhaps this will help.

 

Evolution has 2 critical repeated steps at the very basis of the process.

 

Step one. Create diversity in a population

Step Two. Remove from that population that which is not fit.

or

Step one. Create diversity in a population

Step Two. Remove 99.99% of that diversity.

 

Of course, the theory (NS) can be made to fit almost any senario, but I find this a big ask.

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Michaelangelica: You seem to be considering evolution to be a driving force, it's not, it's a mechanism and it's difficult to see how an alternative mechanism could have allowed complex life to cope. In short, the evolutionary process is itself selected by the problem of continuity of complex life in unstable environments.

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Here's a random thought that occured just now! Darwin's classical work is designated "The origin of species", perhaps at that time the concept of ecoystem was not that well developed. Darwinism that our friends in this thread are discussing is better called "The evolution of ecosystems".

 

Any comments please!!:hyper: :eek2: :eek2:

We have certainly learnt of our interdependence with all life on the planet.

Perhaps something that was not fully appreciated in Darwin's time.

 

My random and probably silly thought:

Where does the junk DNA come from?

Why does a fern or an almost- fish have more genetic material than us?

Is this the remnants of the evolution of life?

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My random and probably silly thought:

Where does the junk DNA come from?

Why does a fern or an almost- fish have more genetic material than us?

Is this the remnants of the evolution of life?

 

I think I have an answer for that!

 

During the thirty odd years of my education I have collected a lots of books. though i was primarily a student of chemistry, but due to my other interests I bought books related to physics, mathematics, biology, psycology, philosophy, literature etc. etc. Fortunately or unfortunately I never has the compulsion of disposing them off. The result is that I have a personal library of hundreds of books, which I seldom use. but, whenever an occasion arises, i have these books at hand for ready reference. many books I have never read, but sometimes I am very interested to read them because they suit the interests at that moment.

 

I think, the so called junk genes have a similar history and purpose.

 

I believe I have contributed something useful in the discussion at hand:) :cup:

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Well we haven't got very far.

Here is a summary of things so far

(selectivly selcted:) )

Originally Posted by Michaelangelica

NATURAL selection is now no longer "natural." It is man made. That has only really happened in earnest in the 20C.

 

For mankind, in all but third world nations, this is true. It is also true of all domesticated animals.

Quote:

… or that modern medicine may have skewed the Whole Harmonious System?

Practitioners of modern medicine (a community of which I consider myself a non-clinician member) are very aware of this possibility.

Quote:

I think random appropriation of interesting genes via bacteria and viruses and blind luck,is a better explanation of evolution than Darwin's Natural Selection. (you can include a bit of it in the 20c mix) It is far too simple and neat a theory.

I don’t think this randomness you describe is incompatible with the theory of natural selection.

It’s important, I think, to keep in mind how little was actually known about the number, structure, and mechanics of genes, and their relationship to observable traits, when Darwin’s theories came to be widely accepted in the mid-to-late 19th century. In light of what we know now, some of the writing of Darwin and his contemporaries seems naive, simplistic, and in some cases, just plain wrong, because they were, just as, in light of future increases in knowledge of molecular biology, much current writing will appear to future readers.

Quote:

Originally Posted by Michaelangelica

It is too pat, too easy. It does not account for what happens in 20C, or what we are learning about DNA.

 

20C is a pretty special time for humanity, that is for certain.

 

Quote:

Originally Posted by Michaelangelica

How does extinction of genetic lines help diversity? Diversity which in turn should help survival of a species?

 

Extinction does not help diversity. Diversity helps prevent extinction.

the Question of diversity

The more diversity the more chance of survival. So why does natural selection reduce diversity?

99.99% of all life that has lived on earth is now extinct. (leaving us with a mere c1.5 million species)

How can this be an efficient sytem? It is a mind-numbingly profligately wasteful system. How can reducing diversity help survival?

To quote Suzuki and Dressel

Quote:

"It is the differences that maximise the chance that there will be survivors under new conditions or different circumstances. Homogencity and monoculture run counter to this basic principle, making us vulnerable to sudden changes.. . .What if there is a mistake?"

and again they quote Tewolde Egziather

Quote:

"If you were to go back to the time of the dinosaurs, and you were to see a little mammal running about, you would never think that this mammal would succeed the dinosaurs. who can tell which is the dinosaur and which is the mammal in our time, in this era of really frightening possibilities?. . .what is successful now and what will be successful in the future. . . is not something linear that proceeds from what we know at the moment (places) have destroyed many of the bridges they would of had into other possibilities.

 

As you say

Quote:

Extinction does not help diversity. diversity helps prevent extinction

Sure the invention of sex gives us diversity but overall diversity is selected against. Why? What part of Darwin explains this phenomenon?

Thus, it is wrong to consider natural selection as the ONLY mechanism of evolution and it is also wrong to claim that natural selection is the predominant mechanism.

Originally Posted by Michaelangelica

What about the very promiscuous bacteria? (most of this planet's life)

How do they choose which bits of another's geonome to appropriate?

The "Natural Selection" model just does not work here.

Organisms like bacteria do appear to confound our usual definitions of “species”, “offspring”, and “individual”.

Questions not answered

Diversity is good for the survival of any species

Agreed?

Why does "Natural Selection" work against diversity?

Again my problem is with the circular nature of the argument.

a good model should be able to PREDICT. Natural selection just conveniently "explains" everything after the event

Quote:

the challenge to evolutionary thinking in recent decades from advocates of Intelligent Design and creationism have impelled many scientists to band together in defense of Darwin's ideas, shoving alternative theories to the background.

 

It seems the attack from the fundamentalist right has stymied the evolution of evolutionary theory (pardon the pun)

What is "the Modern Synthesis of Darwinism,"

Of course, the theory (NS) can be made to fit almost any senario because of the post-hoc and circular nature of the argument. When has the theory acurately predicted an outcome?

How does Darwin account for the fact that 80% of the life on this planet

(Bacteria) can swap genetic material with any other bacteria, no sex involved. They just do it. How do they select which bits to swap?

-- Not all life decides to pass on genes.

Some virus and bacteria just spontaneously die out. Usually because the are too efficient (No 'survival of the fittest' here)

Homosexuals do not tend to pass on their genes.

(We need to assume here that homosexuality is a sociobiological trait like altrusism)

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Michaelangelica last post is crammed with interesting ideas and question, so many it’s hard to pick one to discuss! :shrug:

 

So I’ll start one that I think has an erroneous premise:

Some virus and bacteria just spontaneously die out. Usually because the are too efficient (No 'survival of the fittest' here)
The evolution of bacteria is especially well suited to study, because many bacterial “ecolosystem”, or niches, are self contained, with very well-understood inputs and outputs, because the ratio of bacterial populations is easy to measure, and because bacteria usually compete in a simpler manner than more complicated organisms: the population (of genetically close individuals) that reproduces most quickly grows in relative size, gaining a greater portion of available resources (light and/or energy-providing chemicals, and necessary nutrients), and so become dominant, sometimes to the point of rendering competitors extinct.

 

The key to winning this “game” is metabolic efficiency. Bacteria that spend their available metabolic energy in non-reproductive activities, such as expressing toxin-resist proteins on their cell walls for toxins that don’t exist in their environment, or moving around in a way that doesn’t result in greater intake of resources or avoidance of toxins or other stressors, lose the game to bacteria that don’t. Bacteria that are very reproductively efficient, but that don’t spend energy in sufficient non-reproductive activities to get adequate resources and avoid stressors, die so quickly that their superior reproductive rate can’t be used to advantage, so lose to bacteria that do. The winning bacteria are ones that find an optimum balance between non-reproductive and reproductive activity – in short, the most reproductive efficient bacteria that are able to survive to reproduce, just as predicted by the classical Darwinian “theory” of “survival of the fittest”.

 

This is why a good technique for finding novel bacteria is to introduce toxins – “antibacterials” – into a normal bacterial ecology. The efficient but vulnerable, dominant population is quickly wiped out, allowing the small, crowded-to-the-edges populations to expand rapidly to dominate the nitch.

 

Used unintentionally in the wrong place, however, such as from the misuse of antibacterial cleansers in hospitals and drugs for people with compromised immune systems, this technique is a recipe for medical disaster, and one of the reasons that hospitals are among the most unhealthy places on Earth. The antibiotics/antibacterials can wipe out the benevolent populations of bacteria we are all infested with, allowing novel, often deadlily pathenogenic populations to take their place. :)

Of course, the theory (NS) can be made to fit almost any senario because of the post-hoc and circular nature of the argument. When has the theory acurately predicted an outcome?
My previous description is an example of exactly the kind of post-diction Michaelangelica describes. The observation that natural selection has poor to non-existent performance as a predictive theory leads one to consider whether it’s appropriate to call it a “theory” in the same sense as, for example, the Physics Theory or Relativity. Though use of the word “theory” remains the norm, occasionally biologists, particularly cross-disciplinarian ones with experience in “harder” sciences like physics, referring to it by other terms, such as “paradigm”, “meta-theory”, or “schema”.
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Thanks for the info on bacteria.

I am baseing my assertion on a throw away line of Bill Bryson's (A Short History of Everything) He states that all bacteria can, at will, swap and/or appropriate genetic material from any another bacteria. He questions in fact whether we can call them different individuals!

 

I have just finished reading fantastic book on science that has me thinking like no other. It is By Dr. linda Jean Shepherd and called "Lifting the Veil'

She has couple of interesting things to say about Darwin in passim

CO-OPERATION:When Charles Darwin first presented his theory of evolution to the Linnean Society, he opened his paper with an image of nature as brutal competition: "All nature is at war; one organism with another; or with external nature."

However, there is emerging a cooperative worldview that can stir us to see new connections in nature. . .a .cooperative alliance rather than a cruel and indifferent hunting ground that awards survival only to the fittest individual. . . nature avoids competition by dividing the habitat into ecological niches. Rather than compete for the same food or shelter, species adapt to specific types of food, feeding times, or living conditions.

Another of nature's strategies for peaceful coexistence is voluntary restraint. this flies in the face of the Darwinian model, which maintains that species will increase without limit unless checked by predation, starvation, disease or severe climatic change . . . .stopping ovulation. . .as is the case with mice in overcrowded situations. Animals such as elk, bison, moose, lions, sperm whales and harp seals defer the age of maturity when ever overcrowding occurs

Today, competition drives much of science in order to "maintain national security and economic competitiveness." But fixation on a competitive model blinds us to seeing the cooperative side of nature, best exemplified by symbiosis. This subfield of biology studies organisms living cooperatively together - such as the bacteria living in cows' guts that help digest cellulose. As a science of relationship, symbiosis provides a model of interdependence at the biological level.

 

The work of Lynn Margulis illustrates how a shift in perspective raises radically new questions about nature. She demonstrated that biological diversity arose as much by microbial co-operation as through competition. Initially her theory of cell origins was considered "offensive" and "scandalous" and could not be discussed at respectable scientific meetings. Now biologists agree that mitochondria (energy-producing organelles) were once oxygen-producing bacteria, and that chloroplasts (photosynthesizing organelles) were originally cyanobacteria. These organelles have their own DNA, which is part of the cytoplasmic inheritance of the egg, passed down through the mother line. Margulis maintains that "the major source of evolutionary novelty is the acquisition of symbionts - the whole thing then edited by natural selection. It is never just the accumulation of mutations."

 

In contrast, most theories of evolution still emphasize mutation as the major source of new genetic information. Symbiosis remains an obscure, virtually unfunded, subfield of biology. It is either ignored or merely defined in the major textbooks on evolution.

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I have been reading a bit about Genetic Engineering. Some writers think Darwin is being re-written perhaps to justify GM

I will post something on that soon but it is long and involved and related to Chaos Theory and Quantum and Information Technology.

 

To go back to the basics. Darwin had no idea how "Natural Selection" worked. One of the reasons his early theory was criticised.

It was the re-discovery of Mendel's work on Peas and much later DNA that gave us Neo-Darwinism. ie Darwinism with a mechanism for action.

This mechanism is based on genetic abnormalities where copying of DNA by the cells goes a little wrong but occasionally this gives an environmental advantage.This happens gradually over eons.

 

According to Johnjoe Mc Fadden in "Quantum Evolution", "(the error rate). .is one wrong base for every billion correct bases. . .and their source is quantum mechanical" (hydrogenbond will be pleased)

Now as I read it that is the error rate of all cells. (I would be happy to be proved wrong)

What then is the mathematical chance of an error in the egg or sperm that then gives rise to something worth keeping rather than lethal?.

I'm not much of a mathematician but the odds must be extraordinarily if not impossibly high to account for all the species we find about us

 

Some work by a gentleman called Cairns published an article in science in 1988 saying that cells could CHOOSE the Gene it needed.

 

Other biologists(Stephen Jay Gould and Niles Eldridge) point out that the fossil record does not actually record gradual changes in species.

They suggest that evolution seems to hop and jump, rather than crawl

Also there is STASIS exemplified by crocodiles and Shark Bay W.A. living stromatolites that have changed little or not at all for millions of years.

 

Evolution that goes at two different speeds clearly needs some kind of gearing mechanism to change from one speed to another

 

PS

Does anyone know how to cross sweet peas a la Mendal?

(I would like to try it I am growing 7 varieties this year)

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The following is from the very interesting book The Bio Tech Industry by Jeremy Rifkin. It is a very brief summary of his argument

The historical context of Darwinism

. . .

Charles Darwin's theory of evolution has proven to be a very compatible companion to the Industrial Age.. . . In virtually all the discussions of social Darwinism there is an underlying assumption that the theory itself is disinterested, objective, impartial recording of nature's operating design, untainted by social context and cultural bias.

. . .

a growing number of critics are arguing that his views were heavily influenced by the gestalt of the times

Alex sandow says. . .

. . .Darwinism sprang up where and when capitalism was most strongly established. British Political economy, based on the idea of the survival of the fittest in the marketplace, and the British competitive ethos generally predisposed Britons to think in terms of competitive struggle in theorising about plants and animals as well as man'. . .

. . .

a metaphor for the British marketplace. . .

the same kind of division of labour at work as that found in the English Factory System

. . .

For the millions of Englishmen forced to leave the British isles in the 19C to look for new economic opportunities in alien lands, Darwin's notion of divergence made more than a little sense.

. . .

apparent conflict serves for the benefit of all

. . .

. . .machine imagery. . .

before the age of the machine, living creatures were viewed as "wholes"

. . .

Darwin came to view things as the sum total of parts "assembled" together into more complex and efficient living machines. . .

Darwin was. . 'the application of economics to biology'

. . .

With the publication of The Origin of the Species, the bourgeois could rationalise its economic behaviour by appealing to the universal laws of human nature as its ultimate authority

--

NEXT post( if anyone is listening ) The modern context and Darwin:shrug:

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I have tried to summarise Rifkins ideas here. Basically he believes we are re-inventing our ideas of nature and evolution to justify what we are doing in the Biotech industry.

Just as Darwin's ideas were a product of his own societies' concerns and its self justification of the prevailing economic system

As you can see by the page numbers it is a very brief look at his arguments, so if you are interested go to the source.

The Computer Model of Evolution?

A postmodern cosmology The Biotech Century

 

Our ideas about nature, evolution and and the meaning of life are being re-vamped by the biotech revolution

p187

More biologists are coming to see living organs isms as information systems

. . .life is merely self-programmed activity

. . .p189

Grasse 9says that) the living organism, like the computer, has to be programmed and fed with external information in order for novelties to emerge

. . .

p195

the "molecular computer" a thinking machine made of DNA strands instead of silicon

P216

 

The starship the enterprise contains. .the transporter room

the transporter retains the memory of the original molecular structure of everyone and everything passing through it allowing it to turn information from matter to energy and back to matter again

. . .

The ability to reduce all biological organisms and ecosystems to information and then to use that information to overcome the limitations of time and space is the ultimate dram of biotechnology

. . .

weiner 1950s says all living things are really patterns that perpetuate themsel;ves and that a pattern is a messaage and may be transmitted as a message.

. . .

the new cosmologists would contend that the body is merely a temporary vessel for the information that is embedded in it

. . .

. . .many molecular biologists see the information contained in DNA as immortal (Like a computer memory)

. . .p219

Succeeding generations may well seek after the genomic information embedded in the living processes the way past generations sought after the elixir of life and perpetual motion.

. . .

In the new cosmology it is the information that is made the primary object of attention

. . .p221

We make the rules no need to conform to a set of preexisting cosmic rules.

. . .

Man the architect for the future evolutionary advance of the planet

. . .

bioengineering is not something artificially superimposed on nature but something spawned by nature's own ongoing evolutionary process

. . p.222

together, computer software and genetic wetware represent the ultimate "image making tools" allowing us to use the most sophisticated technics to fashion life into "works of art

. . .p225

I know molecular biologists who sincerely believe that their ability to make changes in the genetic code of living things represents the inevitable next step in the evolutionary process and is unstoppable as natural selection itself

. . .p230

Technologies are not value free

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I have tried to summarise Rifkins ideas here. Basically he believes we are re-inventing our ideas of nature and evolution to justify what we are doing in the Biotech industry….
Like a lot of people my age (b. 1960), I’m familiar with Rifkin’s ideas going back to the 1970s, when he was something of a guru to the emerging green political movement. I’ve written a bit (eg: ”Social transition” in 3799) about “scarcity” and “abundance” economies, terms I encountered in Rifkin.

 

I’ve been on the clinical side of the pharmacy business for a couple of decades (writing and supporting pharmacy computer systems). Biotech, particularly recombinant DNA organism for the production of such drugs as human insulin, has had a revolutionary, and with few exceptions, beneficial impact on humanity – though the business, social and political impact of the pharmacy industry has many negatives. So, along with a lot of folk who were alarmed nearly to the level of fear by Rifkin’s 1970s writing on biotechnology, I’ve become wary of the accuracy and relevance of his observations and predictions, tending to regard Rifkin more as a sort of “non-fictional SF” writer of cautionary tales – a valuable communicator of ideas, but needing to be regarded as very speculative, even when his tone is academic and authoritative.

 

Talk of the convergence of artificial and biological information systems – which I personally believe is occurring and will continue to occur – is a main feature of a school of thought known of late by several terms, such as Extropianism and transhumanism. There are too many fictional and non-fictional writers and writings in this vein to begin to list is a sub-essay post, so I’ll just mention my favorite: Charles Stross’s Accelerando (free for download under a CCL).

 

The truth of the assertion that increased mastery of biotech means the end of natural biological evolution, is, I think, largely a matter of perspective. While science and technology may increasingly understand and selectively improve on natural biology, and may even co-opt biological “Wetware” into nearly or completely artificial systems for engineering or information processing purposes, I think it unlikely that natural biology will be substantially eclipsed or replaced. Natural biology excels at what it does – filling nearly every available ecological niche with life - and is more likely to be imitated – with “tweaks” - than replaced by artificial techniques. Whether one considers the knowledge and control of nature these techniques have and likely will continue to provide to be “the end of nature” or not is, I think, a largely philosophical distinction.

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Thankyou for making me go back and re-read what I thought I knew about Darwin and genetics.

(However I will be more careful in future about throw-away lines. You don't get away with them on hypography)

 

As a result, of this thread, I have just read a most fascinating book that turns on its head most of what I thought i knew about how life develops.

It is called "The Dependent Gene" by a professor of psychology Dr. David S Moore

 

Very briefly his thesis is that all traits- even apparently straightforward ones like eye and hair colour- are caused by very complex interactions between genes and the environment at every stage of biological and psychological development.

 

He rejects the idea that genes set parameters -which the environment fills out - completely

He cites a lot of amazing genetic research

Twin studies, the gold-standard in the nature/nurture debate when I studied psychology, he calls into question completely

He says identical twins are a myth. I was fascinated to read his accounts of in eutro development for twins. It is so complex and intricate. Few twins (30%?)are actually born in the one amniotic sac

 

He argues, convincingly,that the appearance of a given trait is not pre-determined by our genes; but by a very complex and amazing interaction between genes and their environment

 

One study in particular amazed me.

When a chick embryo is a few layers wide; it is known which cells will produce a beak. If you replace the cells UNDERNEATH the beak cells with a mammals cells from a similar position then the chicken will sport a full set of mammalian dentures!

This is despite the fact that the chicken cells that produce the teeth are 100% chicken. It is just being in proximity to the mammalian cells that produces teeth!

"How in the world can this be possible?" he asks. Some biologists explain it by saying genes can lurk unexpressed into our chromosomes for long periods of time, ready to spring into action should factors in their environment suddenly turn them "on".

"It is wrong to assume that there are limitations on a given set of genes before studying their reactions to all possible developmental circumstances."p213

 

"The notion that our genes specify a restricted range of possible developmental outcomes can be of no practical use whatever" p214

 

He says that there is no generally accepted definition of a gene and all the hype in the press about genes to do this or that is just hype. The real story is being found to be far more complex than we ever thought.

(sell your shares in bio-tech companies now!)

 

Fascinating stuff about introns and RNA splicing and e "the spiceosomes in different cells can do different things with the SAME pre-RNA thereby generating two or more different proteins from the code of a single cistron.

Thus spliceosomes can edit a piece of pre RNA, and they can edit this SAME pre RNA in a different cell type to produce an entirely different strand of mature RNA ! p79

Amazingly, cistrons on DNA, too code for immature RNA that can be spliced in different ways in different contexts. . ."

 

Genes, as we usually imagine them, rarely exist in any coherent state in the DNA, waiting to be decoded by automaton like cellular machinery.

Instead, small pieces of DNA-pieces that are not "genes" themselves, because taken individually they do not code for complete functional molecules- are typically mixed matched, and linked to produce various temporary edited RNAs. . .the cellular machinery responsible for this editing is "sensitive" to its context.

 

Such contextual dependence renders untenable the simplistic belief that there are coherent, long -lived entities called "genes" that dictate instructions to cellular machinery that merely constructs the body accordingly.

 

The common belief that genes contain context-independent "information" -and so are analogous to "blueprints" or "recipes"- is simply false' p81

 

He goes on to say that there can be no such thing as a clone.

People who make "clones' like dolly find all sorts of observable differences and personality differences between what should be identical animals.

 

I recommend the book to you.

He does repeat himself over and over but the book contains such an astounding idea that he needs to so that the full implications can begin to set in. This will be a landmark book in evolutionary genetics.

--

On a personal note I have found that pea seeds are fertilised before they are open. So how did Mendel do it and how can I cross my 9 varieties of sweet pea this year?

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Very briefly his thesis is that all traits- even apparently straightforward ones like eye and hair colour- are caused by very complex interactions between genes and the environment at every stage of biological and psychological development.

 

He [Moore] rejects the idea that genes set parameters -which the environment fills out – completely

I’m familiar with this idea under the broad term ”epigenetics”.

 

About ten years ago, it was pretty controversial. One time, on vacation, I discussed some ideas about epigenetics I’d read in a recent Scientific American article with my Molecular Biologist cousin (an older, once removed cousin, and something of an idol of mine when I was as a teenager – she was a “real scientist”, and friends with Carl Sagan!), asking her if she believed there was anything to the idea that something other than embryology – for example, the fluid dynamics of developmental hormones – played a major role in the development of complicated multicellular organisms. She emphatically believed it didn’t. Continued argument came precariously close to provoking a fistfight with her (also a biochemist) boyfriend.

 

The last time I vacationed with them, I enjoyed a good “I told you so” moral victory. The last decade has not only validated epigenetics, but make progress in explaining some of its many complicated mechanisms.

 

A lot of scientific resistance to it was, I think, wishful thinking. The idea that traits were fully determined, combined with advances in automated gene sequencing and computer “bioinformatics”, promised to fully explain functional biology within people’s lifetimes. It’s understandable that people were reluctant to give it up until evidence undeniably demanded it.

 

If Moore is claiming that genetic determinism explains no traits, however, I think he’s going too far. Certainly, some genes express a particular protein, regardless of their endocrinal context. A spectacular example is the insertion of the gene for florescent pigment in jellyfish into mice, with the resulting mice expressing the florescent protein in their skin, and literally glowing in the dark (under a UV light source). (see, for example, http://news.nationalgeographic.com/news/2002/01/0111_020111genmice.html)

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