Should biology be left to the biologists?

[Andy Resnick]

But this is a mistake even many a student of biology make trying to understand evolution. In my study of it, I believe this to be due to our easy ability (probably thanks to evolution! )anthropomorphize everything.

Fair enough- I don't claim to be an expert in modern theories of evolution. I am familiar (in passing only) with the idea of a 'fitness landscape'- I particularly enjoyed Kauffman's "Origins of Order" book.

Some examples of the predictive prowess of evolutionary theory;
<snip>

I only had a chance to look at the antibiotics paper, and it linked to their previos work here:

http://www.genetics.org/cgi/content...e6e0cef6ea851836a298ba0e&keytype2=tf_ipsecsha

I don't think we mean 'predictive' in the same way. For example, using in vitro (forced?) evolution as a predictive model for 'natural' evolution is fine. But surely, the researchers did not predict *which substitutions* would be made by the evolving/mutating bacteria.

As another example- let's say I send you and a <ahem> harem out into space for several generations. We know there are genes that respond to microgravity conditions, and we even know which ones (in a few model organisms). However, I can't predict how your genome will evolve in response to your new environment.

 

[bobze]

Fair enough- I don't claim to be an expert in modern theories of evolution. I am familiar (in passing only) with the idea of a 'fitness landscape'- I particularly enjoyed Kauffman's "Origins of Order" book.
I only had a chance to look at the antibiotics paper, and it linked to their previos work here:

http://www.genetics.org/cgi/content...e6e0cef6ea851836a298ba0e&keytype2=tf_ipsecsha

I don't think we mean 'predictive' in the same way. For example, using in vitro (forced?) evolution as a predictive model for 'natural' evolution is fine. But surely, the researchers did not predict *which substitutions* would be made by the evolving/mutating bacteria.

I see what you mean by "predictive" now. I don't think its that simple though, because mutations are certainly chaotic (I don't use the word random here since certain areas of the genome are more prone to mutation than others, which in itself makes part of the process of mutation "non-random"). However, I don't think because the MS has chaotic elements it cannot be "predictive", it only means you cannot take a reductionist approach.

Similarly, your local weathermen/women are pretty good at predicting weather--So long as we are only talking a few days out, because the inherit chaos in the system (weather systems or over the long term, climate systems).

What I think that a great many biologist have realized over the last half century, is that biology (and its children disciplines) are not reductionist to the degree we can appreciate in physics or chemistry and never will be because of the complexity and chaos of biological systems (not all systems, but the more we "zoom out" the more complex these systems become)--That's the problem with letting all 'you physicists' in on biology, I kid, I kid! There are a seemingly endless supply of variables that make long term predictions (because of inflections and new set points to systems) hard. In the short term though, such predictions to evolutionary change are "doable" (see John Endler's guppies), when we can account for the strongest variables.

That also isn't to say that long term evolutionary change couldn't be predictable, I'd just feel rather sorry for the poor chap that has to write the algorithm

As another example- let's say I send you and a <ahem> harem out into space for several generations. We know there are genes that respond to microgravity conditions, and we even know which ones (in a few model organisms). However, I can't predict how your genome will evolve in response to your new environment.

Right, we don't necessarily "know" how the genome will evolve, but in some cases (short term let's say) we can certainly predict the outcome of the change. Let's consider a more down to Earth example (pun intended . Suppose we took a bunch of white beach mice and transplanted their populations to gradually darker and darker backgrounds while introducing a strong selective pressure introduced by a visual hunter.

We could predict that those mice will get darker and darker coats matching the background and we might even try and predict the changes in the genome that accompany those phenotypical changes. It could be an inactivating mutation in the melanin gene, or a inactivating mutation in the receptor for melanin vacuoles, or the gene for the enzyme which cleaves promelanin, or the gene for the enzyme which activates the promelanin cleavage enzyme, or an even more radical change like the down-regulation of melanin sequestering cells, or or or etc. And if so, where in the gene? Is it a mutation that leads to altered splice sequence, a frame shift, a base deletion?

The problem is then, that evolution has many more solutions to environmental problems than we have the ability to imagine. So the question becomes, which is the more "important" prediction. From the reductionists view probably that "change in the gene", however biology is a "systems game" and the larger "system level" prediction is the one I'd argue is more important here for understanding the biology.

 

[Pythagorean]

I think what Andy was saying is that environment has no formal theoretical framework in the context of biology, so evolution is really only half complete (we have the reductionist/genetic side already going strong)

 

[SW VandeCarr]

In another thread (Are Robots Living Things?) a definition of life was offered which had as one criterion, that living things are made of (biological) cells. I think this is a good example of what the authors (Goldenfeld and Woese) meant regarding in the tendency of biologists to focus on the cell rather than living systems as systems.

Systems in general may be thought of as:

1. Having structure consisting of identifiable components.

2. Having behavior based on inputs, processing and outputs

3. Having interconnectivity of components on which behavior is based.

I would like to hear ideas on how living systems can be defined in these terms. That is, what are the essential (minimal) components of a living system, how to these components interact in terms of inputs, outputs and processing, and what essential interconnectivity is necessary to support these behaviors.

 

[Andy Resnick]

Living systems can repair themselves, at least to some degree.

Living systems also seem to require constant turnover of components- cells, proteins, etc.

 

[SW VandeCarr]

Living systems can repair themselves, at least to some degree.

Living systems also seem to require constant turnover of components- cells, proteins, etc.

OK. That's seems to be a good start. Both repair and maintenance can be thought of in terms of a system's ability to remain in a stable operating state. Both metabolism and replication at smaller scales are involved. Metabolism provides the energy for this. So we can have a system that maintains itself internally and makes copies of some of its components, but may not be able to copy itself in its entirety. So these systems would not qualify as life if we require living systems to make copies of themselves and evolve. Nevertheless such systems would be interesting, especially if they were able to maintain themselves indefinitely within a range of environmental parameters.

Interestingly, hurricanes are simple systems which show limited abilities to repair themselves. They maintain themselves over a short "lifetime" of up to two weeks by extracting energy from the environment, and they exhibit very identifiable structure and behavioral patterns. No one would suggest these things are alive, but they part of a class of systems known as dissipative structures in which some scientists also include living systems.

Individual organisms die, but by making copies of themselves individual living systems are in a sense operating as components in a larger system. That larger system might be a community of similar organisms or an even larger system which we might call an ecology. At this point, it becomes a matter of taste whether you want to call these larger systems "dissipative" if they can last for millions or even billions of years.

My point is that what we might call a living system might be better thought of as a component of a larger sustaining ecology and may be itself a sustaining ecology for a complex of subsystems which could also be called living systems such as individual cells in metazoa.

 

[Ygggdrasil]

I just read a nice essay that's somewhat relevant to the topic of the future of biology and how biologists should be doing research in the future. Here's a short snippet:

Conventionally, biologists have sought to understand life as it exists. Increasingly, however, from stem-cell reprogramming to microbial factories, researchers are describing what is and exploring what could be. An analogous shift occurred in physics and chemistry, especially in the nineteenth century. Like biology, these fields once focused on explaining observed natural processes or material, such as planetary motion or 'organic' molecules. Now they study physical and chemical principles that govern what can or cannot be, in natural and artificial systems, such as semiconductors and synthetic organic molecules.

The expansion of biology from a discipline that focuses on natural organisms to one that includes potential organisms will have three long-term effects. First, it will enlarge the community of biologists to include researchers with different assumptions and goals, such as engineers. Second, it will alter the way in which scientists address the fundamental problem of how biological systems work. Integrating reverse and forward engineering approaches will free biologists to uncover fundamental principles that explain, unify and extrapolate beyond mechanisms observed in specific model systems. Third, it will provide a new conceptual basis for teaching biology — one founded on stimulating inquiry from students as to how biological components and modules could be used to implement complex functions.

Elowitz and Lim. (2010) Build life to understand it. Nature 468: 889. http://dx.doi.org/10.1038/468889a

 

[Andy Resnick]

Elowitz and Lim. (2010) Build life to understand it. Nature 468: 889. http://dx.doi.org/10.1038/468889a

Thanks for the link- nice lego dude,also...

 

[SW VandeCarr]

Here's an interesting short article re a communication out of the U of Illinois,Urbana discussing self assembling charged latex spheres in a saline solution. They're called "Janus" spheres because they carry opposite charges on each side that alternately attract or repel their neighbors. Under the right conditions of salinity they will self assemble into complex structures including helices.

http://www.kurzweilai.net/self-asse...paign=97c0672014-UA-946742-1&utm_medium=email

 

[Andy Resnick]

There are a lot of groups doing cool stuff like that, with all kinds of wacky particles- diblock copolymers, colloidosomes, lithographically patterned nanoparticles, and even DNA (http://www.nature.com/nature/journal/v459/n7245/abs/nature08016.html)

 

[SW VandeCarr]

There are a lot of groups doing cool stuff like that, with all kinds of wacky particles- diblock copolymers, colloidosomes, lithographically patterned nanoparticles, and even DNA (http://www.nature.com/nature/journal/v459/n7245/abs/nature08016.html)

Thanks Andy. I'm not familiar with DNA's uses in nanotechnology. However, I have read about self-replicating nanorobots. I passed it off as interesting but not likely in the near term. Perhaps I'm wrong. What seems to be becoming clear is that the basic components of possible bio-like systems can be quite diverse.