EmbryoPhysics81:: Embryo Physics Course: Diatom morphogenesis

[Richard Gordon]

Wednesday, May 5, 2010 6:06 PM from Winnipeg, MB, Canada

I’m bccing this to the whole Embryo Physics Course mailing list, for those of you who wish to join the dialogue outside of class. Sign up at:

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Yours, -Dick Gordon 

Dear Steve Levin,

Thanks for your comments below. Of course, silica is locally tetrahedral in structure, though I’m not sure how this is disrupted by the nH2O associated with it. The glass illustrated below would seem to have n=0. Biogenic silica is usually represented as Si(OH)4 + nH2O. I reviewed the evidence for microcrystallinity versus amorphous structure of diatom silica on p. 244 of:

Gordon, R. & R.W. Drum (1994). The chemical basis for diatom morphogenesis. Int. Rev. Cytol. 150, 243-372, 421-422. (80MB file, available on request)

 

in terms of the radial distribution function, as determined by x-ray diffraction and other methods, and concluded that there were simply no observations on fresh or live diatom shells, which would be the most relevant. I’d guess that such work still has to be done.

Yes, I agree that regarding the silicalemma (sometimes called silica deposition vesicle) as a membrane bag with no organized material within is not, at first glance, a wise presumption. What we have in the literature are images of isolated, nascent diatom valves versus time, but these only show us the precipitated silica. Such images, from:

Borowitzka, M.A. & B.E. Volcani (1978). The polymorphic diatom Phaeodactylum tricornatum: ultrastructure of its morphotypes. J. Phycol. 14(1), 10-21.

 

are on p.249 of Gordon & Drum (1994). The role of organic matter is in dispute. See:

Gordon, R., D. Losic, M.A. Tiffany, S.S. Nagy & F.A.S. Sterrenburg (2009). The Glass Menagerie: diatoms for novel applications in nanotechnology [invited]. Trends in Biotechnology 27(2), 116-127. (attached)

What the computer simulations suggest is that, given a nucleating center (linear for pennate diatioms, and a small ring for centric diatoms), it is plausible that there is no relevant structure within the silicalemma. Empirical evidence would be nice to have. Conceptually, I would argue that such structure would be deemed a prepattern, whose pattern would then need to be explained. If precipitation of silica proves an adequate explanation for the gross features of the pattern, then why not apply Occam’s razor? Of course, observation trumps a priori reasoning, which is why I call for more observation.

Chaos theory and complexity theory may have their place here, but would not explain the constant features that are shared by daughter cells and bigger clones. Thus they are not easily brought in as an explanation of why and how there are 100,000 morphologically distinct species.

I’m getting mixed messages regarding further interest in diatom morphogenesis and morphogenesis of other single cell organisms, such as ciliates: low attendance today and 3-4 people who couldn’t make it asking me to repeat it. I’ve decided to repeat the talk later and get back to vertebrates next week:

Dick Gordon     Hierarchical Genome: The Whole Megillah in 1 Hour       May 12, 2010
Dick Gordon     Condensed repeat of diatom morphogenesis, + motility (new), in 1 hour        June 9, 2010

The latter date is adjustable on request.

Thanks.

Yours, -Dick 

---------- Forwarded message ----------
From: Stephen M. Levin <sml...@biotensegrity.com>
Date: Wed, May 5, 2010 at 5:56 PM
Subject: Re: Embryo Physics Course: Diatom morphogenesis
To: Richard Gordon <dickgo...@gmail.com>

Dick,   

 From Wikipedia:

The 'local' ordering should  have some structural consequences, after all, it results in a highly organized structure. We are talking about self-organizing structures operating at the mesoscale, and they follow rules of structure (see 'Soft Matter' in Wikipedia). As you point out, in its early stages, the silica is colloidal and soft, and only hardens later, (just like bone does). It sure does look like a hardened foam to me. As noted in my last note to you (enclosed), there may be some collagen involved. Today, you said that the silica may travel along cytoskeletal elements. The silicalema cannot be some bag of amorphous material, I bet it is as highly structures as the cell, which, in my high school days, was a bag of 'fluid' without structure and just some things floating around inside. Levin's Wild Speculation, (See Harris' cartoon):The structure of silica (above) is the 'attractor' that generates the structure of the diatoms' shell, following the rules of fractals, chaos theory and complexity. A minor variation in initial condition would account for the myriad shapes. 

Steve

Dick,

Nice talk on diatoms. It is stuff like that, that stimulates this old brain. Here are some musings from an orthopedic surgeon.

When bone looses its collagen matrix, the hydroxylapatite integrated into its interstices becomes stiff and hard. In death, collagen becomes a stiff and hard ‘rawhide’ glue, (we had a pot of it cooking in my high school woodworking shop). Live bone, a hard foam, (which makes it a ‘soft matter’), is much more flexible than dead bone, and the same can be said of coral. The first time I went snorkeling, I was fascinated to see some of the coral a swaying in the currents. It, too, seems to have a soft matrix that disappears with death and the calcium carbonate exoskeleton of coral becomes stiff and rigid. Silica is the hydroxylapatite of diatoms as calcium carbonate is the hydroxylapatite of coral. What if the exoskeleton of the diatom is also attached to a matrix of soft tissue and only becomes rigid, or seriously rigid, in death?

Bone, as a hard foam, follows the physical laws related to ‘soft matter’, and operates on the mesoscopic scale, http://en.wikipedia.org/wiki/Soft_matter. I would suspect the skeletons of corals and diatoms might also. Once nature develops a plan, it doesn’t often let go.  

Here is a website on silica. According to them, crystals or not, the tetrahedron is the basic building block,  http://academic.brooklyn.cuny.edu/geology/powell/core_asbestos/geology/silicates/intro_min/tet_roll/tetra_roll.htm. 

There are many references to the skeleton of diatoms being ‘tensegrities’. Many of them clearly have the geodesic dome structure that is also seen in fullerene, red blood cells, wbcs, viruses, etc., but to be tensegrities they need the tension component. In bone, it is the collagen matrix that provides it. In diatoms, it would either be the cell itself or a matrix, probably collagen, with the silica integrated into its interstices.

Of course, this is all speculation, but one has to start somewhere.

Steve 

On May 4, 2010, at 9:21 AM, Richard Gordon wrote:

Tuesday, May 4, 2010 8:15 AM from Winnipeg, MB, Canada
Dear Friends,
Tomorrow (Wednesday May 5) I’ll be talking on single cell
morphogenesis whose ornateness would seem to exceed that of many
multicellular organisms, in:

Embryo Physics Course, http://embryophysics.org, most Wednesdays at
2pm Pacific Time, held online at
http://slurl.com/secondlife/Silver%20Bog/84/32/60.

If you need help in getting started in Second Life®
(http://secondlife.com), give me or William R. Buckley a holler:

gor...@cc.umanitoba.ca
W...@wrbuckley.com

Thanks.
Yours, -Dick Gordon

--
Dr. Richard Gordon, Professor, Radiology, University of Manitoba
GA216, HSC, 820 Sherbrook Street, Winnipeg R3A 1R9 Canada
E-mail: gor...@cc.umanitoba.ca, Skype: DickGordonCan, Second Life:
Paleo Darwin, Cell: 1-(204) 995-7125
Embryo Physics Course: http://embryophysics.org/;
http://bookswithwings.ca; Adjunct Scientist: TRLabs, http://www.win.trlabs.ca/
http://www.umanitoba.ca/faculties/medicine/radiology/stafflist/rgordon.html
Affiliate, Institute of Industrial Mathematical Sciences (IIMS),
http://www.umanitoba.ca/institutes/iims/
Principal Scientific Advisor, EvoGrid: http://www.evogrid.org

--
Dr. Richard Gordon, Professor, Radiology, University of Manitoba GA216, HSC, 820 Sherbrook Street, Winnipeg R3A 1R9 Canada
E-mail: gor...@cc.umanitoba.ca, Skype: DickGordonCan, Second Life: Paleo Darwin, Cell: 1-(204) 995-7125
Embryo Physics Course: http://embryophysics.org/;
http://bookswithwings.ca; Adjunct Scientist: TRLabs, http://www.win.trlabs.ca/
http://www.umanitoba.ca/faculties/medicine/radiology/stafflist/rgordon.html
Affiliate, Institute of Industrial Mathematical Sciences (IIMS), http://www.umanitoba.ca/institutes/iims/
Principal Scientific Advisor, EvoGrid: http://www.evogrid.org

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