[hrothgar]

luke warm, on Jun 13 2008, 01:18 PM, said:

Winstonm, on Jun 12 2008, 06:54 PM, said:

Quote

i have a question that probably has a simple answer... has this evolutionary tweak occurred in the past?

My understanding is that a mutation occured in the 10,000 generation but the citrate+ ability was not expressed until the 31,500 generation - showing that total ramdoness led to the evolution of a sophisticated apparatus.

In other words, WTF trumped ID

you don't find it peculiar, even a little, that such a change in e coli hasn't occurred in the billions of years leading up to now, resulting in a quite different specimen in the lab?

Nope

Simplicity is a virtue...

Superfulous organs, pathways, and the like are often evolutionary liabilities and get removed from the system.

Consider cave fish / salamanders as a simple example:

It takes a lot of energy to build / operate an eyeball. This organs is completely useless in a pitch black cave. Guess what happens when a colony of fish spends enough time living in a cave? No more eyeballs.

In a similar vein, its very unclear whether an ability to prcess citrate would provide sufficient advantage in the wild to filter on this genotype... Sure, this mutation might occassionally pop up, however, unless its doing some real good it would probably not establish itself. If it did establish itself it might very well disappear again.

[Winstonm]

luke warm, on Jun 13 2008, 05:18 AM, said:

Winstonm, on Jun 12 2008, 06:54 PM, said:

Quote

i have a question that probably has a simple answer... has this evolutionary tweak occurred in the past?

My understanding is that a mutation occured in the 10,000 generation but the citrate+ ability was not expressed until the 31,500 generation - showing that total ramdoness led to the evolution of a sophisticated apparatus.

In other words, WTF trumped ID

you don't find it peculiar, even a little, that such a change in e coli hasn't occurred in the billions of years leading up to now, resulting in a quite different specimen in the lab?

No.
Neither do I believe it sinister that this happened now in a lab.

[jtfanclub]

luke warm, on Jun 13 2008, 05:18 AM, said:

you don't find it peculiar, even a little, that such a change in e coli hasn't occurred in the billions of years leading up to now, resulting in a quite different specimen in the lab?

Part of the definition of E. coli is that it can't process citrates. So if it had mutated into something that can process citrates (like amoebas or humans) then it wouldn't be E. coli any more.

It's like saying "Isn't it odd that lizards in billions of years have never mutated to lose their limbs?" They have. We just don't call them lizards any more. We call them snakes.

[luke warm]

jtfanclub, on Jun 13 2008, 10:44 AM, said:

luke warm, on Jun 13 2008, 05:18 AM, said:

you don't find it peculiar, even a little, that such a change in e coli hasn't occurred in the billions of years leading up to now, resulting in a quite different specimen in the lab?

Part of the definition of E. coli is that it can't process citrates. So if it had mutated into something that can process citrates (like amoebas or humans) then it wouldn't be E. coli any more.

It's like saying "Isn't it odd that lizards in billions of years have never mutated to lose their limbs?" They have. We just don't call them lizards any more. We call them snakes.

now that makes sense

[Al_U_Card]

Isn't it just another one of those "mysterious" ways?

[barmar]

jtfanclub, on Jun 13 2008, 11:44 AM, said:

luke warm, on Jun 13 2008, 05:18 AM, said:

you don't find it peculiar, even a little, that such a change in e coli hasn't occurred in the billions of years leading up to now, resulting in a quite different specimen in the lab?

Part of the definition of E. coli is that it can't process citrates. So if it had mutated into something that can process citrates (like amoebas or humans) then it wouldn't be E. coli any more.

Right. There's an article in this month's Scientific American about how we determine what is and isn't a species, and asexually reproducing organisms cause lots of headaches for taxonomists.

In the real world we look at traits like the food an organism can metabolize. On the other hand, it's hard to argue that the "child" of an E. coli is not another E. coli, as is its grandchild, great grandchild, and so on for thousands of generations. After enough mutations you eventually have to decide that you've got a different species, but evolution is usually so gradual that it's normally impossible to pinpoint the moment that speciation happened.

It's like the transition from day to night. Noon is certainly daytime, midnight is nighttime, but around dusk there's no exact moment when you can say "A second ago it was light, now it's dark." In fact, nature has very few exact dividing lines. Humans like to have them, but they're usually set arbitrarily for convenience (e.g. using the 18th or 21st birthday as the transition from child to adult for legal purposes).

[helene_t]

barmar, on Jun 14 2008, 06:14 AM, said:

There's an article in this month's Scientific American about how we determine what is and isn't a species, and asexually reproducing organisms cause lots of headaches for taxonomists. [.....]
In fact, nature has very few exact dividing lines.  Humans like to have them, but they're usually set arbitrarily for convenience (e.g. using the 18th or 21st birthday as the transition from child to adult for legal purposes).

Yes, this widespread obsession with putting things in categories is a pet peeve of mine. To some extent because of my work as a medical statistician, I have to deal with data that have been corrupted by people who think it's smart to reduce continues scales such as blood pressure into arbitrary categories such as "low, normal, high".

Just read a part of Ernst Mayr's "The growth of biological thought". He asks the question why Darwin came later than Newton while Darwin's problem was easier to solve. His answer is that the Darwinian revolution needed a major philosophical shift because the idea of one species evolving from another contradicts the Platonian doctrine of essentialism which had dominated Western philosophy from the antique until quite recently.

Personally I am skeptical. I think your example with day vs night is so obvious that even the most stubborn platonist must have been open to the thought that our categorization of living things may to some extent be based on arbitrary thresholds. I would rather say that Darwin's problem was more difficult than Newton's.

Anyway, it is a fascinating read.

[barmar]

helene_t, on Jun 14 2008, 10:34 AM, said:

barmar, on Jun 14 2008, 06:14 AM, said:

There's an article in this month's Scientific American about how we determine what is and isn't a species, and asexually reproducing organisms cause lots of headaches for taxonomists. [.....]
In fact, nature has very few exact dividing lines.  Humans like to have them, but they're usually set arbitrarily for convenience (e.g. using the 18th or 21st birthday as the transition from child to adult for legal purposes).

Yes, this widespread obsession with putting things in categories is a pet peeve of mine. To some extent because of my work as a medical statistician, I have to deal with data that have been corrupted by people who think it's smart to reduce continues scales such as blood pressure into arbitrary categories such as "low, normal, high".

Just read a part of Ernst Mayr's "The growth of biological thought". He asks the question why Darwin came later than Newton while Darwin's problem was easier to solve. His answer is that the Darwinian revolution needed a major philosophical shift because the idea of one species evolving from another contradicts the Platonian doctrine of essentialism which had dominated Western philosophy from the antique until quite recently.

Personally I am skeptical. I think your example with day vs night is so obvious that even the most stubborn platonist must have been open to the thought that our categorization of living things may to some extent be based on arbitrary thresholds. I would rather say that Darwin's problem was more difficult than Newton's.

Anyway, it is a fascinating read.

Categorizing seems to be a necessary evil, to allow efficient thought processes. The brain works by linking concepts together, and if everything were treated continuously there wouldn't be places to hang those concepts. The brain is, to some extent, digital -- a signal either does or doesn't fire across any particular synapse. Living is all about making concrete decisions: should I do X or Y?

I can appreciate that simplification like this doesn't make things easier for you as a statistician. But think of it from the perspective of the doctor actually making a diagnosis. Trying to juggle lots of detailed numbers in his head would be overwhelming, while dealing with things like "high/low blood pressure" or "does/doesn't have a fever" makes it manageable.

Perhaps it would be possible to design a brain that could keep track of such level of details. But there's little reason why evolution would have done so. Our ancestors never needed to keep detailed statistics, and categorization works extremely well for normal decision making. When you're just trying to survive, it's unlikely to make a difference how you categorize an animal that happens to be the cusp between two species -- you pick one and get on with your life.

Getting back to the original subtopic, I'm looking forward to reading Microcosm: E. coli and the New Science of Life by Carl Zimmer, which just arrived yesterday from Amazon.

[helene_t]

barmar, on Jun 14 2008, 05:39 PM, said:

I can appreciate that simplification like this doesn't make things easier for you as a statistician.

The thing is, to me it is not a simplification. Consider the relation between two continous variables. One of the simplest things I can think of is a bivariate normal distribution. The phycisians seem to prefer something like "is X is in range A then there is a probability p(Q|A) that Y is in range Q etc. Sometimes I think intuitively in categories, but at other times I think in continous scales.

Sometimes a binary decision has to be made. We don't give half a heart transplant to a patient with half the need for a heart transplant. So in decision models, categories must be introduced at some stage. But what annoys me is that people seem to think that reality is made a categories.

I think it is mainly a language thing. Language is digital for the same reason that electronic communication protocols are. It is much easier to talk about categories than about continous scales. Even when discussing with phycisist I find it difficult to talk about continious scales, and we will often need pen and paper because the concepts can be communicated only in the form of written formulas.

We are generally able to handle decision processes that require thinking in continous scales, though, even though people often say things like "I related in this way to older people and that way to younger people".

Penrose wrote something in "The emperor's new mind" that I found intriguing. Concerning the debate of whether language is a prerequisite to consciousness, he said that philosophers often assume that to be the case while scientists/mathematicians more often assume that consciousness came first and language later. He attributed it to the fact that he as a mathematician thinks in terms of concepts that cannot be verbalized, while he suspects that philosophers who work with verbalized concepts think by the aid of an "inner voice" and therefore find it hard to imagine thinking without language.

[Winstonm]

Quote

He attributed it to the fact that he as a mathematician thinks in terms of concepts that cannot be verbalized, while he suspects that philosophers who work with verbalized concepts think by the aid of an "inner voice" and therefore find it hard to imagine thinking without language.

That is rather interesting. I know I am extremely language-based, i.e., I learn best from reading, and I hear an "inner voice" that comprises my thinking. I never stopped to think others may not have this same inner voice.

[barmar]

Winstonm, on Jun 14 2008, 05:45 PM, said:

Quote

He attributed it to the fact that he as a mathematician thinks in terms of concepts that cannot be verbalized, while he suspects that philosophers who work with verbalized concepts think by the aid of an "inner voice" and therefore find it hard to imagine thinking without language.

That is rather interesting. I know I am extremely language-based, i.e., I learn best from reading, and I hear an "inner voice" that comprises my thinking. I never stopped to think others may not have this same inner voice.

This certainly seems like a difficult problem, which came first, language or high-level concepts? I'm sure even Penrose hears language most of the time when he talks to himself (like deciding what to have for dinner), but maybe he's more visual when he thinks about mathematical concepts. I also imagine that many of us wonder what it's like to think like a dog or cat (every time I see a spider on my car windshield, I wonder what it thinks when we get to our destination, miles away from its home). It's probably similar to what babies think about, but I doubt many of us can remember what it was like to think before we could verbalize.

[barmar]

barmar, on Jun 14 2008, 12:39 PM, said:

Getting back to the original subtopic, I'm looking forward to reading Microcosm: E. coli and the New Science of Life by Carl Zimmer, which just arrived yesterday from Amazon.

So I started reading the book this afternoon, and what do you know, he has a couple of paragraphs about entropy, echoing what we've been saying:

Quote

As E. coli juggles iron, captures energy, and transforms sugar into complex molecules, it seems to defy the universe.  There's a powerful drive throughout the universe, known as entropy, that pushes order toward disorder. ... E. Coli seems to push against the universe, assembling atoms into intricate proteins and genes and preserving that orderliness from one generation to the next.  It's like a river that flows uphill.

E. coli is not really so defiant.  It is not sealed off from the rest of the universe.  It does indeed reduce its own entropy, but only by consuming energy it gets from outside.  And while E. coli increases its own internal order, it adds to the entropy of the universe with its heat and waste.  On balance, E. coli actually increases entropy, but it manages to bob on the rising tide.

E. coli's metabolism is a microcosm of life as a whole.

[PassedOut]

Approaching the 150th anniversary of the publication of Darwin's masterpiece, the New York Times has an Olivia Judson piece today putting his work into historical perspective: Darwinmania!

Quote

Before the “Origin,” the diversity of life could only be catalogued and described; afterwards, it could be explained and understood. Before the “Origin,” species were generally seen as fixed entities, the special creations of a deity; afterwards, they became connected together on a great family tree that stretches back, across billions of years, to the dawn of life. Perhaps most importantly, the “Origin” changed our view of ourselves. It made us as much a part of nature as hummingbirds and bumblebees (or humble-bees, as Darwin called them); we, too, acquired a family tree with a host of remarkable and distinguished ancestors.

The reason the “Origin” was so powerful, compelling and persuasive, the reason Darwin succeeded while his predecessors failed, is that in it he does not just describe how evolution by natural selection works. He presents an enormous body of evidence culled from every field of biology then known...

Of course Darwin knew that his work would disturb some folks (including his wife), but we have all benefited immensely from it.

[helene_t]

barmar, on Jun 15 2008, 02:20 AM, said:

I'm sure even Penrose hears language most of the time when he talks to himself (like deciding what to have for dinner), but maybe he's more visual when he thinks about mathematical concepts.

Cannot speak for Penrose, but I don't use an inner voice when thinking about dinner. I think in terms of images of the ingredients, where in the supermarket they are, and the cooking process. Maybe this is related to the thing that I never read cook books but just open the fridge and see what is there and which of the things in the fridge I feel like eating, and whether I feel like eating it raw or boiled etc.

I do think by the aid of an inner voice when ding logical reasoning, such as when playing bridge and at my work. And when I think how to communicate things to others, of course. I used to share a lot of thoughts with my mother so my inner voice would often be speaking to my mother. This is still the case although she died 14 years ago.

Maybe the thing that I don't have a language I consider "my language" make me a less verbal thinker. I usually think in Dutch or English but neither of those is my native language so I miss words for many concepts.

A friend of mine who studies philosophy says she never needs an inner voice when solving the problems they puzzle with during logics classes. She just "sees" the solution. This is curious since she has no college training in math (and probably didnt open a math book for 25 years).

[Sigi_BC84]

helene_t, on Jun 14 2008, 07:13 PM, said:

Sometimes a binary decision has to be made. We don't give half a heart transplant to a patient with half the need for a heart transplant. So in decision models, categories must be introduced at some stage. But what annoys me is that people seem to think that reality is made a categories.

I think it is mainly a language thing. Language is digital for the same reason that electronic communication protocols are. It is much easier to talk about categories than about continous scales.

You are touching something very deep and profound here.

We're so used to categorizing the world that we mistake our categories for "reality" (which, quite ironically, is just another category, albeit a very abstract and elusive one; in fact it doesn't even exist as such).

Decision models obviously need categories, as you can't even start to build a model of anything without adapting a dualistic view of the world and giving names to things and so on. These models are useful and necessary, and natural, in many ways. However, I don't think that decision making requires categorical thinking. We often make intuitive decisions and they are not necessarily worse than rational ones (sometimes they're even better). So if you meant to say the latter, I think I'll have to disagree.

Language enters the picture (of perception, categorizing, forming of self-consciousness) very, very early and I think that (cognitive/neuro) science still has a looong way to go to give some definitive answers to questions like "which came first, language or high-level concepts?" The best efforts currently made involve deep introspection, and while I consider that very valid it's unfortunately useless when applying scientific standards.

This is all very vague, but there is an inspiring book touching many of these topics called Shifting Worlds, Changing Minds by Jeremy Hayward. It deals with modem cognitive science and Buddhism (the author is a scientist with a background in molecular biology and also a Buddhist teacher). The text is very scientific but targetted at a general audience. You will most certainly like it if you liked Penrose's book and Hofstadter's works.

[PassedOut]

The New York Times today has a nice piece about a science teacher in Florida -- ex-Navy pilot David Campbell -- working hard to overcome the anti-evolution forces in his state: A Teacher on the Front Line as Faith and Science Clash

Quote

In February, the Florida Department of Education modified its standards to explicitly require, for the first time, the state’s public schools to teach evolution, calling it “the organizing principle of life science.” Spurred in part by legal rulings against school districts seeking to favor religious versions of natural history, over a dozen other states have also given more emphasis in recent years to what has long been the scientific consensus: that all of the diverse life forms on Earth descended from a common ancestor, through a process of mutation and natural selection, over billions of years.

Campbell worked hard to help Florida create the new standards:

Quote

...at the inaugural meeting of the Florida Citizens for Science, which he co-founded in 2005, he vented his frustration. “The kids are getting hurt,” Mr. Campbell told teachers and parents. “We need to do something.”

The Dover decision in December of that year dealt a blow to “intelligent design,” which posits that life is too complex to be explained by evolution alone, and has been widely promoted by religious advocates since the Supreme Court’s 1987 ban on creationism in public schools. The federal judge in the case called the doctrine “creationism re-labeled,” and found the Dover school board had violated the constitutional separation of church and state by requiring teachers to mention it. The school district paid $1 million in legal costs.

Inspired, the Florida citizens group soon contacted similar groups in other states advocating better teaching of evolution. And in June 2007, when his supervisor invited Mr. Campbell to help draft Florida’s new standards, he quickly accepted.

During the next six months, he made the drive to three-day meetings in Orlando and Tallahassee six times. By January 2008 the Board of Education budget had run out. But the 30 teachers on the standards committee paid for their own gasoline to attend their last meeting.

Mr. Campbell quietly rejoiced in their final draft. Under the proposed new standards, high school students could be tested on how fossils and DNA provide evidence for evolution. Florida students would even be expected to learn how their own species fits into the tree of life.

In teaching the new standards, though, Campbell has to work with students heavily influenced by creationists.

Quote

The last question on the test Mr. Campbell passed out a week later asked students to explain two forms of evidence supporting evolutionary change and natural selection.

“I refuse to answer,” Bryce wrote. “I don’t believe in this.”

In his classes, Campbell distinguishes between religious belief and science. He tells his students that they don't have to believe in evolution, but they do have to understand it.

Quote

When the bell rang, he knew that he had not convinced Bryce, and perhaps many of the others. But that week, he gave the students an opportunity to answer the questions they had missed on the last test. Grading Bryce’s paper later in the quiet of his empty classroom, he saw that this time, the question that asked for evidence of evolutionary change had been answered.

[Trinidad]

If we make a good understanding of evolution theory a mandatory requirement to graduate from high school two things can happen.

1) Non-evolutionists will be at a disadvantage and be less adapted to the circumstances. Eventually only evolutionists remain, thus giving evidence for evolution theory.

2) The Lord will take good care of the steadfast creationists and they will prevail, thus giving evidence for creationism.

I say we do the experiment for about a century and then we will decide.

Rik

[helene_t]

Sigi_BC84, on Jun 21 2008, 04:55 AM, said:

Decision models obviously need categories, as you can't even start to build a model of anything without adapting a dualistic view of the world and giving names to things and so on. These models are useful and necessary, and natural, in many ways. However, I don't think that decision making requires categorical thinking. We often make intuitive decisions and they are not necessarily worse than rational ones (sometimes they're even better). So if you meant to say the latter, I think I'll have to disagree.

I think you are right. Obviously, intuition plays a larger role in everyday life than do formal decision models. A friend of mine set off to find out (as part of her Ph.D. thesis) if physicians, when making actual decisions, rely on the (irrational) dichotomus models described in their standards, or more rational Bayesian approaches. The jury is still out, of course, since there will hardly be a simple answer to such a big question, but so far it seems to her that physicians are more rational, and less black-and-white thinking, than the textbook models. However, at the conscious level, people seem to deal with lots of illusory cathegories. For example, most people think the question "how many colors are there in the rainbow?" makes sense objectively.

Quote

I think that (cognitive/neuro) science still has a looong way to go to give some definitive answers to questions like "which came first, language or high-level concepts?"  The best efforts currently made involve deep introspection, and while I consider that very valid it's unfortunately useless when applying scientific standards.

In Stephen Pinker's "How the mind works", some evidence is presented for language being secondary to concepts. For example, children being born deaf and not taught reading or sign language appear to develop concepts nonetheless. Of course this does not settle the question of which came first in human evolution. My intuition would be that the two have evolved hand-in-hand over tens of thousands of years.

Quote

Shifting Worlds, Changing Minds by Jeremy Hayward

Thanks, I will get a copy!

Rik: I don't think your experiment will settle anything. As a scientist, I can easily think of a mechanism by which natural selection would favor belief in Creationism and other irrational ideas. Conversely, I am sure a biblical literalist could think of a reason for god to want people to believe in evolution.

[jtfanclub]

PassedOut, on Aug 24 2008, 10:38 AM, said:

Quote

In February, the Florida Department of Education modified its standards to explicitly require, for the first time, the state’s public schools to teach evolution, calling it “the organizing principle of life science.” Spurred in part by legal rulings against school districts seeking to favor religious versions of natural history, over a dozen other states have also given more emphasis in recent years to what has long been the scientific consensus: that all of the diverse life forms on Earth descended from a common ancestor, through a process of mutation and natural selection, over billions of years.

I know, it's not your quote, and it's not David's quote, but it still bugs me to hear lines like 'that all of the diverse life forms on Earth descended from a common ancestor'.

But there's no real evidence for that, and no requirement in Evolution that this be so. That would imply that there was only a single occurrence of life forming from not-life on the planet, at least which has descendents still living in the world. Is it really necessary to Evolution, for example, that fungi and plants have a common ancestor? Why couldn't they each have evolved independently?

I'm sure they do, but there are sulphur bacteria undersea volcanos....
http://www.arctic.no...essay_vogt.html
http://science.nasa....ad16sep98_1.htm

which I suspect have no common ancestors with 'regular' life forms. They evolved in a completely different environment, and seem to have little in common with ordinary bacteria.

To me, it feels almost religious to say everything has a common ancestor. Who's to say that various carbon chains can together coincidentally to create life in what is now the Pacific Ocean, and that the same thing happened a hundred million years later in what is now the Atlantic Ocean? Actually, it seems that the archaebacteria came first, and the eubacteria came much later, and it's not clear at all to me that the latter evolved from the former. The archaebacteria seem to me to be an ecological dead end.

[barmar]

jtfanclub, on Aug 24 2008, 10:17 PM, said:

But there's no real evidence for that, and no requirement in Evolution that this be so. That would imply that there was only a single occurrence of life forming from not-life on the planet, at least which has descendents still living in the world. Is it really necessary to Evolution, for example, that fungi and plants have a common ancestor? Why couldn't they each have evolved independently?

No, it's not *necessary*. In fact, it's quite common for different evolutionary paths to produce similar results -- eyes and wings have evolved independently in many different lineages.

Once evolution gets going, it can do remarkable things. But getting it going seems to be much harder. Evolutionary biologists still haven't figured out where the initial spark came from. But it probably requires very special conditions, and once there's an ecosystem going, it would probably be very hard for a new form of life to gain a foothold.

Anything is possible, but I don't think any indication of a second tree of life has been found. All the life we know of is based on the same DNA nucleotides and the way it encodes proteins. We've decodes genomes of many organisms, from bacteria and viruses to homo sapiens, and there's far too much in common for anything other than common descent to be the explanation. By comparing genertic codes, scientists can actually work evolution backwards, and figure out approximately when the evolutionary trees of two species branched apart from their common ancestor.