Understanding Biology


by crownedbishop
Tags: biology
crownedbishop
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#1
Feb18-14, 02:53 PM
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So, I have a biology and physics question that I don't really understand. I go to physics class, and they talk about atoms, and particles, and what we can do with them. I understand that. Then I go to biology class, and they start talking about cells, DNA, RNA, and they talk about individual parts of a cell as if it has a purpose, and they fulfill their purposes as if they choose to do them. I asked my biology professor why they do what they do, and she spouts off something about how they have evolved to act this way. I ask my physics professor, and he tells me something about how it's because of big bang cosmology, and just as quarks were made from energy, this is the way things are because it is from the high information state from before the big bang. He said evolution doesn't really come into play unless you try to isolate it because it is such a small factor, it really comes from the information. This just made me think I didn't really understand evolution after all. So, was my physics professor right? Was my biology professor right? Or neither? I really don't understand.
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Pythagorean
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#2
Feb18-14, 03:25 PM
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On the one hand, your physics professor is talking about the fundamental properties of matter and energy, which is a natural thing for a physicist to do. I wouldn't agree with him that evolution is a "small factor". I would say evolution (and biology) are emergent behaviors. So it's all physics: matter behaves in this way or that way, even matter in biological systems, but biological systems represent are specific class of molecular dynamics and physics that has properties most other physical systems in the known universe don't have (replication, adaptation, etc.) and, in my opinion, evolution is a big part of what differentiates them from other molecular processes.

When people talk about purpose with cells, it's a short-hand way to talk about why that particular kind of dynamics survived (passed the tests of natural selection). Cells aren't thought to actually have intentions.
Ygggdrasil
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#3
Feb18-14, 05:21 PM
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When considering "why" questions in biology, we usually consider answers on one of two scales: proximate causes and ultimate causes, discussed by Ernst Mayr in his classic paper, Cause and Effect in Biology.

The proximate cause for a specific trait or behavior relates to the physiological mechanisms that give rise to the trait. For example, if we consider the example question from Mayr's essay, why do birds migrate south for the winter, the proximate cause relates to birds' ability to sense the length of days and how this photoperiod sensing interacts with innate genetic circuits. While many biologists discuss proximate causes in terms of genes and genetics, proximate causes are in principle understandable in terms of chemistry and physics (e.g. protein x interacts with protein y to cause reaction z to occur).

Ultimate causes in biology relate why a certain trait or behavior evolved. In the case of the migration of birds, migration evolved because the birds' food sources become scarce in the winter, so to survive most birds will migrate to warmer climates where they can find food to survive. Often times, these ultimate causes are ecological in nature and deal with the interaction of a species with the environment and the other species around it, and therefore, it is not really useful to think about these ultimate causes at the level of basic physics and chemistry.

Can you understand biology without considering evolution? Sure, you can understand biology in terms of proximate causes only and be able to explain a lot of biological phenomena. But considering proximate causes only gives an incomplete picture of biology and would be akin to studying physics by memorizing a set of formula without knowing their derivations or studying organic chemistry by memorizing a list of reactions without knowing the reaction mechanisms.

crownedbishop
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#4
Feb19-14, 11:24 PM
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Understanding Biology


Well, you don't need the derivations of the physics formulas. They would be fine if the physics worked exactly like the formula says. There's no need to understand what they mean, they are mathematical statements that will give true predictions. However, we could equally claim that the migration evolved because of the information from before the big bang instead of from scarcity of food. Pythagorean, when you say evolution is an emergent behavior, is it because of the statistical likeliness of that behavior to survive. Or analogous to perhaps the statistical likeliness of entropy to increase?
Romulo Binuya
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#5
Feb20-14, 07:43 AM
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Erwin Schrodinger was a physicist and one of the founding fathers of Quantum Mechanics. He made a foray into biology and tried to answer the question "how can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?".

He wrote a lecture about it titled "What is Life?". Although some of the notions in the lecture have been superseded by modern science, it's interesting to see how great mind works.. he laid out the theoretical description of the DNA and how it work. There is a free pdf download of "What is Life?" lecture in the external link section of the wikipedia for those who are interested to read it.
http://en.wikipedia.org/wiki/What_Is_Life%3F
Pythagorean
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#6
Feb20-14, 08:15 AM
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Quote Quote by crownedbishop View Post
Pythagorean, when you say evolution is an emergent behavior, is it because of the statistical likeliness of that behavior to survive. Or analogous to perhaps the statistical likeliness of entropy to increase?
I just mean there's nothing new in terms of fundamental physics going on. But with the physics we already have there's still thousands of complicated systems we could set up depending on the ratios of forces, the geometry of the matter, and the energy dynamics. When such systems display new behaviors (without any fundamentally new physics) we call those behaviors emergent.
Ygggdrasil
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Feb20-14, 03:45 PM
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Quote Quote by crownedbishop View Post
However, we could equally claim that the migration evolved because of the information from before the big bang instead of from scarcity of food.
This implies a great deal of determinism in the universe, which I am not sure is the case. You are essentially stating that if you were to exactly recreate the events of the big bang, the universe would come out exactly the same to the level of the behavior of a particular species on a particular planet in the copy of our universe. While this may very well be true, it also seems like there are many points at which some random fluctuation played some role in altering the history of the universe. Galaxies, solar systems, and planets form at spots where the density of interstellar material just happens to be greater than in surrounding areas. The preponderance of matter over anti-mater in the observable universe could be another result of a random fluctuation as could the preponderance of L-amino acids and D-sugars in terrestrial biology.

Indeed, an interesting question in evolutionary biology is the extent to which evolution is deterministic. If we "replay the tape of life" that is, re-create the identical conditions of prebiotic Earth would evolution play out in the same way? This is very much an active field of research, but from my reading of the literature, it seems like random events have had important effects on the evolutionary history of many species and that evolution does not occur completely deterministically.

For a nice review of this topic, see Lobkovsky and Koonin. 2012. Replaying the Tape of Life: Quantification of the Predictability of Evolution. Front Genet 3: 246. doi:10.3389/fgene.2012.00246 PMCID:3509945
kpapp
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#8
Feb24-14, 11:14 AM
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Biology is ubiquitous, opportunistic, has no intention. That makes it seem to make "decisions", "choices" and be "creative".

It is a higher level functioning system than physics, which stops at the size of atomic level. Fundamental physics describes smaller but not larger combinations of atoms and atomic effects, such as solar storms and gravity.
Feeble Wonk
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#9
Feb28-14, 06:42 PM
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Biological structure and function very definitely are a result of evolution. But yes, physics drives chemistry, which drives biochemistry which in turn drives molecular biology. Some would suggest that the "physics" part is largely limited to the thermodynamics of the system providing energy to "make things happen", with most biological processes being at an emergent higher level of organization. Regardless, there is no "intentionality" in this process, if by that you mean that it is a purposeful, goal oriented action. In fact, it is quite possible that you could even make that statement with regard to human consciousness. Because, in the end, it is all physics, and physical determinism appears to be absolute.
Romulo Binuya
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#10
Mar3-14, 08:03 PM
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Schrodinger thought that the genome is the material carrier of life. Life that circumvent the second law of thermodynamics within the spatial boundary of the living organism, and life is the difference between a living organism and a pile of molecules.

Dr. Craig Venter said life is information system within the genome. I'm not yet convinced albeit Dr. Venter and his team at the JCVI created the world's first cyborg bacterium which is made of a surrogate cell and a synthetic genome. Did the synthetic genome assimilated the cell or is it the cell that assimilated the synthetic genome and gave life to it? Most probably Dr. Venter is right, life is information system... and they synthesized it. http://www.gizmag.com/first-syntheti...created/15165/
Feeble Wonk
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#11
Mar3-14, 08:15 PM
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I'd have to agree... and take that one step farther. All of physical existence is really about information storage and evolution, and biological systems are the most complicated and information rich examples of that process.
Romulo Binuya
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#12
Mar4-14, 12:21 AM
P: 64
Imo both the physics professor and the biology professor in the OP are both correct. Considering, the idea that "if it can happen, it will happen!" is fundamental to quantum mechanics.. although the probability is very very low that the atoms of the genome will be configured that way by themselves, still the probability is not zero... and it did happen :D
gravenewworld
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#13
Mar12-14, 05:09 PM
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The first thing to understand when learning biology is to throw the central dogma of biology (DNA to RNA to Protein) in the trash. The human genome only has 25,000 genes which absolutely can not explain the complexity of a cell. There are 400+ post translational modifications (some of which are vastly more complex than what DNA can encode) all acting in concert to control protein expression, function, trafficking, half life, you name it. All of which is non-template driven with no code that can be controlled like DNA. The real complexity of a cell (and life) is explained how all of this produces millions of distinct molecular entities at any given moment in time and how these millions of different molecular species are fine tuned to achieve homeostasis and proper physiology.
Romulo Binuya
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#14
Mar13-14, 02:46 AM
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They did flushed the abiogenesis research down the relevance toilet, but picked up again sometime in 2007 and eventually discovered additional amino acids. There is something wrong with their replication of the primordial mud soup, the same forces that configured those amino acids would destroy any genome hence no spontaneous emergence of life was demonstrated yet. Maybe they will keep on trying although the probability is very very low to produce the ancestors of the glorified apes. That is science anyways, the established rules of empirical, stable, and demonstrable protocol.
Ryan_m_b
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#15
Mar13-14, 08:10 AM
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Quote Quote by Romulo Binuya View Post
They did flushed the abiogenesis research down the relevance toilet, but picked up again sometime in 2007 and eventually discovered additional amino acids. There is something wrong with their replication of the primordial mud soup, the same forces that configured those amino acids would destroy any genome hence no spontaneous emergence of life was demonstrated yet. Maybe they will keep on trying although the probability is very very low to produce the ancestors of the glorified apes. That is science anyways, the established rules of empirical, stable, and demonstrable protocol.
I'm sorry but I don't understand. Who are you talking about? Which studies were these? Please post references so others can see where you are coming from with regards to abiogenesis.
Romulo Binuya
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#16
Mar13-14, 09:22 AM
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The Miller–Urey experiment in1953 is the most successful in abiogenesis, at least to me. http://en.wikipedia.org/wiki/Miller–Urey_experiment
Pythagorean
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#17
Mar13-14, 09:26 AM
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But who is "they" and how did they "flush it down the toilet". I'm not really sure what your point is either. I assure you that Ryan and I are both familiar with the Miller-Urey experiment.
Romulo Binuya
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#18
Mar14-14, 04:01 AM
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"They" refers to everyone who are against abiogenesis. The phrase "flush it down the relevance toilet" is just a metaphor, another way of saying consider it irrelevant, ignore, disregard, or neglect. My post was written that way to tell that I understood post #13 especially its key words.. dogma of biology... throw to the thrash.. fined tuned... complexity. Nice to know that you're familiar with miller-urey experiment... about the reluctance of the publisher to publish it.. and miller didn't got the Nobel despite his nominations.


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